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diff --git a/src/Cargo.lock b/src/Cargo.lock
index c08ff779..e7554bb6 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -1658,6 +1658,7 @@ dependencies = [
  "obikalgorithm",
  "obikindex",
  "obikindexer",
+ "obikmerge",
  "obikseq",
  "obipipeline",
  "obiread",
@@ -1672,13 +1673,15 @@ name = "obikmerge"
 version = "0.1.0"
 dependencies = [
  "obicompactvec",
- "obikfilter",
+ "obikalgorithm",
  "obikindex",
  "obikindexer",
  "obikseq",
  "obipipeline",
  "obiskio",
  "obisys",
+ "rayon",
+ "tempfile",
  "tracing",
 ]
 
diff --git a/src/obikidxcache/src/index_cache.rs b/src/obikidxcache/src/index_cache.rs
index 53d9aaec..bd6a517a 100644
--- a/src/obikidxcache/src/index_cache.rs
+++ b/src/obikidxcache/src/index_cache.rs
@@ -1,56 +1,80 @@
+use std::collections::HashMap;
+
 use obikindex::{KmerIndex, layer::KmerLayer};
 use obikseq::CanonicalKmer;
 
 use crate::meta_cache::MetaCache;
 
 pub struct IndexCache<'a> {
+    /// Ties this cache's lifetime to the `KmerIndex` it was opened from —
+    /// borrow-checker-enforced, not just documentation: an `IndexCache`
+    /// cannot outlive its index, so it can never be read against an index
+    /// that has since been mutated or dropped. `index()` is a genuine
+    /// accessor, but the field's real job is this lifetime bound, kept even
+    /// on paths that never call `index()`.
     raw_index: &'a KmerIndex,
     meta: MetaCache,
 
-    n_partition: usize,
-    n_layer: usize,
-    layer_cache: Vec<KmerLayer>,
+    /// Keyed by each partition's own index number, not renumbered —
+    /// `partitions: Some(vec![5])` still reads back as partition `5`
+    /// everywhere (`get_layer(5, ..)`, `find_in_partition(5, ..)`, …), not
+    /// `0`. A `HashMap` rather than a flat `Vec` because the set of cached
+    /// partitions doesn't have to be `0..n_partitions`, or even contiguous
+    /// — see [`new`](Self::new).
+    layer_cache: HashMap<usize, Vec<KmerLayer>>,
 }
 
 impl<'a> IndexCache<'a> {
-    /// Opens every layer of every partition once, up front, and keeps them
-    /// alive for the cache's lifetime — `layer(p, l)` stored flat at
-    /// `p * n_layer + l` (`n_layer` uniform across partitions, guaranteed by
-    /// construction).
+    /// Opens every layer of the given `partitions` (every partition of the
+    /// index, if `None`) once, up front, and keeps them alive for the
+    /// cache's lifetime — each partition's own layer count is read
+    /// independently (`KmerPartition::n_layers`), so partitions don't need
+    /// a uniform layer count across each other. That matters for a caller
+    /// like `obikmerge`, which only ever needs one specific partition of a
+    /// destination index still being merged into elsewhere — the other
+    /// partitions can legitimately have a different layer count at that
+    /// moment (built in parallel, mid-run), without that affecting a cache
+    /// scoped to just the one partition being read.
     ///
-    /// Panics if the index isn't fully built: a cache can only be built on a
-    /// functional index, so any failure here (missing/incomplete layer) is a
-    /// caller error, not a case to design around with a `Result`.
-    pub fn new(index: &'a KmerIndex) -> Self {
-        let n_partition = index.n_partitions();
-        let n_layer = index.n_layers_per_partition().unwrap_or_else(|e| {
-            panic!("IndexCache::new: index is not fully built (n_layers_per_partition failed): {e}")
-        });
+    /// Panics if any requested partition fails to open (e.g. an
+    /// out-of-range partition number, or a layer that fails to open): a
+    /// cache can only be built on partitions that actually exist and are
+    /// complete, so any failure here is a caller error, not a case to
+    /// design around with a `Result`.
+    pub fn new(index: &'a KmerIndex, partitions: Option<Vec<usize>>) -> Self {
+        let selected = partitions.unwrap_or_else(|| (0..index.n_partitions()).collect());
 
-        let mut layer_cache = Vec::with_capacity(n_partition * n_layer);
-        for p in 0..n_partition {
+        let mut layer_cache = HashMap::with_capacity(selected.len());
+        for p in selected {
+            let partition = index
+                .partition(p)
+                .unwrap_or_else(|e| panic!("IndexCache::new: failed to open partition {p}: {e}"));
+            let n_layer = partition.n_layers();
+            let mut layers = Vec::with_capacity(n_layer);
             for l in 0..n_layer {
-                let layer = index
-                    .layer(p, l)
-                    .and_then(KmerLayer::open)
-                    .unwrap_or_else(|e| {
-                        panic!(
-                            "IndexCache::new: failed to open layer (partition {p}, layer {l}): {e} — index is not fully built"
-                        )
-                    });
-                layer_cache.push(layer);
+                let layer = partition.layer(l).and_then(KmerLayer::open).unwrap_or_else(|e| {
+                    panic!(
+                        "IndexCache::new: failed to open layer (partition {p}, layer {l}): {e} — partition is not fully built"
+                    )
+                });
+                layers.push(layer);
             }
+            layer_cache.insert(p, layers);
         }
 
         IndexCache {
             raw_index: index,
             meta: MetaCache::from_meta(&index.meta()),
-            n_partition,
-            n_layer,
             layer_cache,
         }
     }
 
+    /// The index this cache was opened from.
+    #[inline]
+    pub fn index(&self) -> &'a KmerIndex {
+        self.raw_index
+    }
+
     /// The index's metadata, snapshotted once at construction — see
     /// [`MetaCache`]. Read-only
     #[inline]
@@ -58,31 +82,41 @@ impl<'a> IndexCache<'a> {
         &self.meta
     }
 
+    /// Number of layers cached for `partition` — `None` if `partition`
+    /// isn't part of this cache.
     #[inline]
-    pub fn n_layer(&self) -> usize {
-        self.n_layer
+    pub fn n_layer(&self, partition: usize) -> Option<usize> {
+        Some(self.layer_cache.get(&partition)?.len())
     }
 
+    /// Number of partitions cached — not necessarily `raw_index.n_partitions()`
+    /// when this cache was built on a subset (see [`new`](Self::new)).
     #[inline]
     pub fn n_partition(&self) -> usize {
-        self.n_partition
+        self.layer_cache.len()
+    }
+
+    /// Which partitions this cache holds, in no particular order.
+    pub fn partitions(&self) -> impl Iterator<Item = usize> + '_ {
+        self.layer_cache.keys().copied()
     }
 
     #[inline]
     pub fn get_layer(&self, partition: usize, layer: usize) -> Option<&KmerLayer> {
-        self.layer_cache.get(partition * self.n_layer + layer)
+        self.layer_cache.get(&partition)?.get(layer)
     }
 
     pub fn iter(&self) -> impl Iterator<Item = &KmerLayer> {
-        self.layer_cache.iter()
+        self.layer_cache.values().flatten()
     }
 
     pub fn iter_indexed(&self) -> impl Iterator<Item = (usize, usize, &KmerLayer)> {
-        let n_layer = self.n_layer;
-        self.layer_cache
-            .iter()
-            .enumerate()
-            .map(move |(i, layer)| (i / n_layer, i % n_layer, layer))
+        self.layer_cache.iter().flat_map(|(&p, layers)| {
+            layers
+                .iter()
+                .enumerate()
+                .map(move |(l, layer)| (p, l, layer))
+        })
     }
 
     #[inline]
@@ -99,19 +133,25 @@ impl<'a> IndexCache<'a> {
     /// goes through `KmerLayer::find_slot`'s evidence check, not a blind
     /// MPHF lookup.
     #[inline]
-    pub fn find_in_layer(&self, partition: usize, layer: usize, kmer: CanonicalKmer) -> Option<usize> {
+    pub fn find_in_layer(
+        &self,
+        partition: usize,
+        layer: usize,
+        kmer: CanonicalKmer,
+    ) -> Option<usize> {
         self.get_layer(partition, layer)?.find_slot(kmer)
     }
 
-    /// Membership-checked lookup across every layer of one partition —
-    /// first layer that carries `kmer` wins. `None` if `partition` is out
-    /// of range or no layer of it carries `kmer`.
+    /// Membership-checked lookup across every cached layer of one
+    /// partition — first layer that carries `kmer` wins. `None` if
+    /// `partition` isn't cached or no layer of it carries `kmer`.
     pub fn find_in_partition(
         &self,
         partition: usize,
         kmer: CanonicalKmer,
     ) -> Option<(usize, usize, usize)> {
-        for l in 0..self.n_layer {
+        let n_layer = self.n_layer(partition)?;
+        for l in 0..n_layer {
             if let Some(slot) = self.find_in_layer(partition, l, kmer) {
                 return Some((partition, l, slot));
             }
@@ -119,14 +159,17 @@ impl<'a> IndexCache<'a> {
         None
     }
 
-    /// Membership-checked lookup across every partition and layer — first
-    /// one that carries `kmer` wins.
+    /// Membership-checked lookup — routes `kmer` straight to its one
+    /// possible partition (`CanonicalKmer::partition`, the same
+    /// minimizer-hash rule every k-mer was scattered by when the index was
+    /// built) instead of scanning every cached partition: a k-mer can only
+    /// ever live in the partition it hashes to, so anywhere else is not
+    /// worth even asking. Uses `self.index().n_partitions()` — the index's
+    /// real total, not [`n_partition`](Self::n_partition) (this cache's own
+    /// count, which can be a subset — see [`new`](Self::new)). `None` if
+    /// that partition isn't cached or doesn't carry `kmer`.
     pub fn find(&self, kmer: CanonicalKmer) -> Option<(usize, usize, usize)> {
-        for p in 0..self.n_partition {
-            if let Some(hit) = self.find_in_partition(p, kmer) {
-                return Some(hit);
-            }
-        }
-        None
+        let partition = kmer.partition(self.raw_index.n_partitions());
+        self.find_in_partition(partition, kmer)
     }
 }
diff --git a/src/obikidxcache/src/layered_store.rs b/src/obikidxcache/src/layered_store.rs
deleted file mode 100644
index 4747af87..00000000
--- a/src/obikidxcache/src/layered_store.rs
+++ /dev/null
@@ -1,100 +0,0 @@
-use ndarray::{Array1, Array2};
-use rayon::prelude::*;
-
-use obicompactvec::traits::{BitPartials, ColumnWeights, CountPartials};
-
-/// A store that aggregates a `Vec<S>` — one entry per layer (within a partition)
-/// or one entry per partition.
-///
-/// Blanket impls of `ColumnWeights`, `CountPartials`, and `BitPartials` propagate
-/// automatically: `LayeredStore<LayeredStore<S>>` implements the same traits as
-/// `LayeredStore<S>`, giving the partitioned level for free.
-pub struct LayeredStore<S>(pub Vec<S>);
-
-impl<S> LayeredStore<S> {
-    pub fn new(layers: Vec<S>) -> Self { Self(layers) }
-    pub fn layers(&self) -> &[S] { &self.0 }
-    pub fn n_layers(&self) -> usize { self.0.len() }
-    pub fn is_empty(&self) -> bool { self.0.is_empty() }
-}
-
-// ── ColumnWeights ─────────────────────────────────────────────────────────────
-
-impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> {
-    fn col_weights(&self) -> Array1<u64> {
-        self.0.par_iter()
-            .map(|s| s.col_weights())
-            .reduce_with(|a, b| a + b)
-            .unwrap_or_else(|| Array1::zeros(0))
-    }
-}
-
-// ── CountPartials ─────────────────────────────────────────────────────────────
-
-impl<S: CountPartials> CountPartials for LayeredStore<S> {
-    fn partial_bray(&self) -> Array2<u64> {
-        self.0.par_iter()
-            .map(|s| s.partial_bray())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-
-    fn partial_euclidean(&self) -> Array2<f64> {
-        self.0.par_iter()
-            .map(|s| s.partial_euclidean())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-
-    fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
-        self.0.par_iter()
-            .map(|s| s.partial_threshold_jaccard(threshold))
-            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
-            .unwrap()
-    }
-
-    fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
-            .map(|s| s.partial_relfreq_bray(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-
-    fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
-            .map(|s| s.partial_relfreq_euclidean(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-
-    fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.0.par_iter()
-            .map(|s| s.partial_hellinger(global))
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-}
-
-// ── BitPartials ───────────────────────────────────────────────────────────────
-
-impl<S: BitPartials> BitPartials for LayeredStore<S> {
-    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
-        self.0.par_iter()
-            .map(|s| s.partial_jaccard())
-            .reduce_with(|(ai, au), (bi, bu)| (ai + bi, au + bu))
-            .unwrap()
-    }
-
-    fn partial_hamming(&self) -> Array2<u64> {
-        self.0.par_iter()
-            .map(|s| s.partial_hamming())
-            .reduce_with(|a, b| a + b)
-            .unwrap()
-    }
-}
-
-// ── Tests ─────────────────────────────────────────────────────────────────────
-
-#[cfg(test)]
-#[path = "tests/layered_store.rs"]
-mod tests;
diff --git a/src/obikindex/src/layer/content_layer.rs b/src/obikindex/src/layer/content_layer.rs
index c318ab0a..f38784d3 100644
--- a/src/obikindex/src/layer/content_layer.rs
+++ b/src/obikindex/src/layer/content_layer.rs
@@ -240,6 +240,26 @@ impl KmerLayer {
         }
     }
 
+    // content_layer.rs, à côté de fill_sub_matrix_carries
+    /// Batch, genome-major column extraction — `out[g][i]` = genome `g`'s raw
+    /// value at `slots[i]` (count as-is, presence promoted to 0/1). Column-first,
+    /// like the underlying storage: one read pass per genome column, not one per
+    /// kmer.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<u32>]) {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.fill_sub_matrix(slots, out),
+            KmerLayer::Presence { layer, .. } => {
+                let mut bools: Vec<Vec<bool>> = out.iter().map(|_| Vec::new()).collect();
+                layer.fill_sub_matrix(slots, &mut bools);
+                for (o, b) in out.iter_mut().zip(bools.iter()) {
+                    o.clear();
+                    o.extend(b.iter().map(|&v| v as u32));
+                }
+            }
+            KmerLayer::Empty { .. } => panic!("Layer::fill_sub_matrix() called on an Empty layer"),
+        }
+    }
+
     /// Raw MPHF lookup: kmer → slot, no membership check.
     pub fn hash(&self, kmer: CanonicalKmer) -> usize {
         match self {
diff --git a/src/obikindex/src/layer/mphf_layer.rs b/src/obikindex/src/layer/mphf_layer.rs
index ce16c2b7..7721ebac 100644
--- a/src/obikindex/src/layer/mphf_layer.rs
+++ b/src/obikindex/src/layer/mphf_layer.rs
@@ -412,6 +412,12 @@ impl MphfOnly {
     pub fn index(&self, kmer: CanonicalKmer) -> usize {
         self.0.index(&kmer.raw())
     }
+
+    /// Batch form of [`index`](Self::index) — one MPHF lookup pass over the
+    /// whole slice instead of one call per kmer.
+    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        kmers.iter().map(|&k| self.index(k)).collect()
+    }
 }
 
 impl MphfLayer {
diff --git a/src/obikindex/src/partition/mod.rs b/src/obikindex/src/partition/mod.rs
index f134422e..f5ad037b 100644
--- a/src/obikindex/src/partition/mod.rs
+++ b/src/obikindex/src/partition/mod.rs
@@ -61,7 +61,7 @@ pub struct KmerPartition {
 impl KmerPartition {
     pub fn new(index: &KmerIndex, i: usize) -> Self {
         KmerPartition {
-            partition_dir: index.dir().join(format!("part_{i:05}")),
+            partition_dir: index_dir(index.dir(), i),
             id: i,
         }
     }
diff --git a/src/obikmer2/Cargo.toml b/src/obikmer2/Cargo.toml
index 8937e705..b08c0eab 100644
--- a/src/obikmer2/Cargo.toml
+++ b/src/obikmer2/Cargo.toml
@@ -15,6 +15,7 @@ obisys        = { path = "../obisys" }
 obikindex     = { path = "../obikindex", default-features = false }
 obikindexer   = { path = "../obikindexer" }
 obikalgorithm = { path = "../obikalgorithm" }
+obikmerge     = { path = "../obikmerge" }
 obifastwrite  = { path = "../obifastwrite" }
 obiskbuilder  = { path = "../obiskbuilder" }
 clap          = { version = "4", features = ["derive"] }
diff --git a/src/obikmer2/src/cmd/merge/mod.rs b/src/obikmer2/src/cmd/merge/mod.rs
new file mode 100644
index 00000000..d1545e7d
--- /dev/null
+++ b/src/obikmer2/src/cmd/merge/mod.rs
@@ -0,0 +1,104 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikalgorithm::Algorithm;
+use obikindex::KmerIndex;
+use obikmerge::{Merge, MergeMode};
+use obisys::{Progress, Reporter, Stage, progress_bar};
+use tracing::info;
+
+#[derive(Args)]
+pub struct MergeArgs {
+    /// Source index directories to merge
+    #[arg(required = true)]
+    pub sources: Vec<PathBuf>,
+
+    /// Output index directory
+    #[arg(short, long)]
+    pub output: PathBuf,
+
+    /// Overwrite output directory if it already exists
+    #[arg(long, default_value_t = false)]
+    pub force: bool,
+
+    /// Force presence/absence mode even if all sources have count data
+    #[arg(long, default_value_t = false)]
+    pub force_presence: bool,
+
+    /// Disambiguate duplicate genome labels by appending .1, .2, … instead of erroring
+    #[arg(long, default_value_t = false)]
+    pub rename_duplicates: bool,
+}
+
+pub fn run(args: MergeArgs) {
+    let sources: Vec<KmerIndex> = args
+        .sources
+        .iter()
+        .map(|p| {
+            info!("opening source index: {}", p.display());
+            KmerIndex::open(p).unwrap_or_else(|e| {
+                eprintln!("error opening source index {}: {e}", p.display());
+                std::process::exit(1);
+            })
+        })
+        .collect();
+
+    // Auto-detect mode: count if all sources have count data, presence otherwise.
+    // --force-presence overrides to presence regardless.
+    let all_have_counts = sources.iter().all(|s| s.meta().config.with_counts);
+    let mode = if !args.force_presence && all_have_counts {
+        MergeMode::Count
+    } else {
+        MergeMode::Presence
+    };
+    info!(
+        "merge mode: {}",
+        if mode == MergeMode::Count {
+            "count"
+        } else {
+            "presence/absence"
+        }
+    );
+
+    let source_refs: Vec<&KmerIndex> = sources.iter().collect();
+
+    let n_genomes: usize = sources
+        .iter()
+        .map(|s| {
+            s.meta()
+                .genomes()
+                .unwrap_or_else(|e| {
+                    eprintln!("error reading index metadata: {e}");
+                    std::process::exit(1);
+                })
+                .len()
+        })
+        .sum();
+    info!(
+        "merging {} index(es), {} genome(s) total → {}",
+        sources.len(),
+        n_genomes,
+        args.output.display()
+    );
+
+    let mut rep = Reporter::new();
+    let t = Stage::start("merge");
+    let n_partitions = source_refs.first().map(|s| s.n_partitions()).unwrap_or(0);
+    let pb = progress_bar("merge", n_partitions as u64, "partitions");
+
+    let mut merge = Merge::new(&source_refs, &args.output, mode)
+        .force(args.force)
+        .rename_duplicates(args.rename_duplicates)
+        .on_progress(|_: Progress| pb.inc(1));
+
+    let dst = merge.run().unwrap_or_else(|e| {
+        eprintln!("error merging: {e}");
+        std::process::exit(1);
+    });
+    pb.finish_and_clear();
+    rep.push(t.stop());
+
+    info!("merge done — output at {}", dst.dir().display());
+    merge.reporter().print();
+    rep.print();
+}
diff --git a/src/obikmer2/src/cmd/mod.rs b/src/obikmer2/src/cmd/mod.rs
index 2547bc25..307cf14d 100644
--- a/src/obikmer2/src/cmd/mod.rs
+++ b/src/obikmer2/src/cmd/mod.rs
@@ -1,2 +1,3 @@
 pub mod index;
+pub mod merge;
 pub mod superkmer;
diff --git a/src/obikmer2/src/main.rs b/src/obikmer2/src/main.rs
index 9ec8afb8..501f9901 100644
--- a/src/obikmer2/src/main.rs
+++ b/src/obikmer2/src/main.rs
@@ -17,6 +17,8 @@ enum Commands {
     Index(cmd::index::IndexArgs),
     /// Extract super-k-mers from input sequences and scatter them by partition
     Superkmer(cmd::superkmer::SuperkmerArgs),
+    /// Merge multiple genome indexes into one
+    Merge(cmd::merge::MergeArgs),
 }
 
 fn main() {
@@ -31,5 +33,6 @@ fn main() {
     match cli.command {
         Commands::Index(args) => cmd::index::run(args),
         Commands::Superkmer(args) => cmd::superkmer::run(args),
+        Commands::Merge(args) => cmd::merge::run(args),
     }
 }
diff --git a/src/obikmerge/Cargo.toml b/src/obikmerge/Cargo.toml
index 1620c3c9..fb9890bc 100644
--- a/src/obikmerge/Cargo.toml
+++ b/src/obikmerge/Cargo.toml
@@ -6,10 +6,14 @@ edition = "2024"
 [dependencies]
 obikindex     = { path = "../obikindex" }
 obikindexer   = { path = "../obikindexer" }
-obikfilter    = { path = "../obikfilter" }
+obikalgorithm = { path = "../obikalgorithm" }
 obicompactvec = { path = "../obicompactvec" }
 obiskio       = { path = "../obiskio" }
 obikseq       = { path = "../obikseq" }
 obipipeline   = { path = "../obipipeline" }
 obisys        = { path = "../obisys" }
+rayon         = "1"
 tracing       = "0.1.44"
+
+[dev-dependencies]
+tempfile = "3"
diff --git a/src/obikmerge/src/lib.rs b/src/obikmerge/src/lib.rs
index 89d51a79..8f30fd03 100644
--- a/src/obikmerge/src/lib.rs
+++ b/src/obikmerge/src/lib.rs
@@ -1,17 +1,19 @@
 //! Merging multiple `obikindex::KmerIndex` sources into one: bootstrapping
-//! from the first source, then merging each remaining source partition by
-//! partition (de Bruijn graph union + column fill). A maintenance/
+//! from a chosen base source, then merging each remaining source partition
+//! by partition (de Bruijn graph union + column fill). A maintenance/
 //! transformation operation on already-built indexes, not part of the
 //! `Index { Partition { Layer } }` data model itself — kept out of
 //! `obikindex` so that crate doesn't grow this algorithm's own
 //! dependencies (`obipipeline`, `obidebruinj` via `obikindexer`).
 //!
-//! [`merge_layer`] holds the per-partition merge primitive
-//! (`merge_partition`, `SrcLayerData`) — the latter is also reused by
-//! `obikrebuild::rebuild_layer`, hence its `pub` visibility here.
+//! Structured on the model of `obikindexer::algorithms`: [`Merge`]
+//! implements `obikalgorithm::Algorithm` (two-phase `new` + setters, then
+//! `run`). Pass 2 of [`partition_merge::merge_partition`] reads each source
+//! layer through `obikindex::layer::KmerLayer` directly, batched
+//! column-first via `KmerLayer::fill_sub_matrix` — no merge-local matrix
+//! wrapper needed.
 
 mod merge;
-mod merge_layer;
+mod partition_merge;
 
-pub use merge::*;
-pub use merge_layer::{MergeMode, SrcLayerData};
+pub use merge::{Merge, MergeMode};
diff --git a/src/obikmerge/src/merge.rs b/src/obikmerge/src/merge.rs
index c428a94b..e4c5a120 100644
--- a/src/obikmerge/src/merge.rs
+++ b/src/obikmerge/src/merge.rs
@@ -1,22 +1,25 @@
 use std::collections::HashMap;
 use std::fs;
 use std::io;
-use std::path::Path;
+use std::path::{Path, PathBuf};
 
-use obikindex::IndexBuilder;
+use obikalgorithm::Algorithm;
+use obikindex::layer::IndexMode;
+use obikindex::partition::PARTITIONS_SUBDIR;
+use obikindex::{GenomeInfo, IndexBuilder, IndexState, KmerIndex};
 
-use obisys::{Reporter, Stage, progress_bar, spinner};
+use obisys::{PartitionRunner, Progress, Reporter, Stage};
 use tracing::{debug, info};
 
-use obikindex::layer::IndexMode;
+use crate::partition_merge::merge_partition;
 
-use obikindex::{OKIError, OKIResult};
-use obikindex::KmerIndex;
-use obikindex::{GenomeInfo, IndexMeta};
-use obikindex::IndexState;
-use obisys::PartitionRunner;
+// ── MergeMode ─────────────────────────────────────────────────────────────────
 
-pub use crate::merge_layer::MergeMode;
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+pub enum MergeMode {
+    Presence,
+    Count,
+}
 
 // ── per-partition diagnostic record ──────────────────────────────────────────
 
@@ -27,58 +30,117 @@ struct PartStat {
     g_len: usize,
 }
 
-// ── main merge entry point ────────────────────────────────────────────────────
+// ── Merge — two-phase construction, `Algorithm` shape ─────────────────────────
 
-impl KmerIndex {
-    pub fn merge<P: AsRef<Path>>(
-        output: P,
-        sources: &[&KmerIndex],
-        mode: MergeMode,
-        force: bool,
-        rename_duplicates: bool,
-        budget_fraction: f64,
-        rep: &mut Reporter,
-    ) -> OKIResult<Self> {
-        let output = output.as_ref();
+/// Merges `sources` into a new index at `output`. Bootstraps from whichever
+/// source can host the merge unapproximated (see [`choose_base`]) via
+/// `KmerIndex::create` + `set_genomes` — `config` is written once, at
+/// creation, never patched afterward, same invariant every other
+/// construction path (`create_skeleton`) already holds. Then merges each
+/// remaining source into the bootstrap destination, partition by partition,
+/// via [`merge_partition`].
+pub struct Merge<'a> {
+    sources: &'a [&'a KmerIndex],
+    output: PathBuf,
+    mode: MergeMode,
+    force: bool,
+    rename_duplicates: bool,
+    reporter: Reporter,
+    on_progress: Option<Box<dyn FnMut(Progress) + Send + 'a>>,
+}
+
+impl<'a> Merge<'a> {
+    pub fn new(sources: &'a [&'a KmerIndex], output: impl Into<PathBuf>, mode: MergeMode) -> Self {
+        Self {
+            sources,
+            output: output.into(),
+            mode,
+            force: false,
+            rename_duplicates: false,
+            reporter: Reporter::new(),
+            on_progress: None,
+        }
+    }
+
+    /// Remove a pre-existing index at `output` before creating the merged
+    /// one (default: `false`, fails if one already exists).
+    pub fn force(mut self, v: bool) -> Self {
+        self.force = v;
+        self
+    }
+
+    /// Disambiguate duplicate genome labels across sources by suffixing
+    /// `.1`, `.2`, ... instead of failing (default: `false`).
+    pub fn rename_duplicates(mut self, v: bool) -> Self {
+        self.rename_duplicates = v;
+        self
+    }
+
+    /// Progress callback, called once per completed partition.
+    pub fn on_progress(mut self, cb: impl FnMut(Progress) + Send + 'a) -> Self {
+        self.on_progress = Some(Box::new(cb));
+        self
+    }
+
+    /// Per-stage timing report accumulated during `run` (bootstrap,
+    /// spectrums, merge_partitions, finalize) — call after `run` returns.
+    pub fn reporter(&self) -> &Reporter {
+        &self.reporter
+    }
+}
+
+impl Algorithm for Merge<'_> {
+    type Output = KmerIndex;
+
+    fn run(&mut self) -> obikalgorithm::Result<KmerIndex> {
+        let output = self.output.clone();
+        let sources = self.sources;
 
         if sources.is_empty() {
-            return Err(OKIError::Io(io::Error::new(
+            return Err(io::Error::new(
                 io::ErrorKind::InvalidInput,
                 "merge requires at least one source index",
-            )));
+            )
+            .into());
         }
 
         // ── Validate config compatibility ─────────────────────────────────────
         let ref0 = sources[0];
         for src in sources {
             if src.state()? != IndexState::Indexed {
-                return Err(OKIError::NotIndexed(src.root_path.clone()));
+                return Err(format!("{}: source index is not fully built", src.dir().display()).into());
             }
             if src.kmer_size() != ref0.kmer_size()
                 || src.minimizer_size() != ref0.minimizer_size()
                 || src.n_partitions() != ref0.n_partitions()
             {
-                return Err(OKIError::IncompatibleConfig);
+                return Err("merge sources have incompatible k-mer size / minimizer size / partition count".into());
             }
-            if mode == MergeMode::Count && !src.meta.config.with_counts {
-                return Err(OKIError::MismatchedMode);
+            if self.mode == MergeMode::Count && !src.meta().config.with_counts {
+                return Err(format!(
+                    "{}: source index has no per-genome counts, cannot merge in count mode",
+                    src.dir().display()
+                )
+                .into());
             }
         }
 
         // Read each source's genome list once — `IndexMeta::genomes` is a
         // fresh disk read every call, so cache it rather than re-reading it
         // repeatedly through the rest of this function.
-        let src_genomes: Vec<Vec<GenomeInfo>> =
-            sources.iter().map(|s| s.genomes()).collect::<OKIResult<_>>()?;
+        let src_genomes: Vec<Vec<GenomeInfo>> = sources
+            .iter()
+            .map(|s| s.meta().genomes())
+            .collect::<io::Result<_>>()?;
 
         // ── Log source characteristics and choose base ────────────────────────
-        let mode_str = if mode == MergeMode::Presence {
+        let mode_str = if self.mode == MergeMode::Presence {
             "presence"
         } else {
             "count"
         };
         info!(
-            "merge: {} source(s), smer-size={}, mode={}",
+            "merge: {} source(s), kmer-size={}, mode={}",
             sources.len(),
             sources[0].kmer_size(),
             mode_str,
@@ -89,7 +151,7 @@ impl KmerIndex {
             } else {
                 format!("{} genomes", src_genomes[i].len())
             };
-            let trivial_str = if is_trivial(&src_genomes[i], mode) {
+            let trivial_str = if is_trivial(&src_genomes[i], self.mode) {
                 " [trivial: no data approximation]"
             } else {
                 ""
@@ -97,32 +159,28 @@ impl KmerIndex {
             info!(
                 "  [{}] {} — {}, {}, {}{}",
                 i,
-                src.root_path.display(),
-                format_evidence(&src.meta.config.evidence),
+                src.dir().display(),
+                format_evidence(&src.meta().config.evidence),
                 genome_str,
                 mode_str,
                 trivial_str,
             );
         }
 
-        let base_idx = choose_base(sources, &src_genomes, mode);
+        let base_idx = choose_base(sources, &src_genomes, self.mode);
         let needs_approx = sources.iter().enumerate().any(|(i, src)| {
-            !is_trivial(&src_genomes[i], mode)
+            !is_trivial(&src_genomes[i], self.mode)
                 && matches!(
-                    src.meta.config.evidence,
+                    src.meta().config.evidence,
                     IndexMode::Approx { .. } | IndexMode::Hybrid { .. }
                 )
         });
         info!(
             "output evidence: {} ({}base: [{}] {})",
-            format_evidence(&sources[base_idx].meta.config.evidence),
-            if needs_approx {
-                "forced approx — "
-            } else {
-                ""
-            },
+            format_evidence(&sources[base_idx].meta().config.evidence),
+            if needs_approx { "forced approx — " } else { "" },
             base_idx,
-            sources[base_idx].root_path.display(),
+            sources[base_idx].dir().display(),
         );
 
         let mut ordered: Vec<&KmerIndex> = Vec::with_capacity(sources.len());
@@ -137,56 +195,56 @@ impl KmerIndex {
         }
         let sources: &[&KmerIndex] = &ordered;
         let src_genomes = ordered_genomes;
-        let evidence = sources[0].meta.config.evidence.clone();
+        let evidence = sources[0].meta().config.evidence.clone();
 
         // ── Compute final genome labels ────────────────────────────────────────
-        let (source_labels, all_genomes) = compute_labels(&src_genomes, rename_duplicates)?;
+        let (source_labels, all_genomes) = compute_labels(&src_genomes, self.rename_duplicates)?;
 
         // ── Prepare output directory ──────────────────────────────────────────
-        KmerIndex::clear_output_for_create(output, force)?;
+        KmerIndex::clear_output_for_create(&output, self.force)?;
 
-        // ── Bootstrap: copy first source to output ────────────────────────────
+        // ── Bootstrap: create the destination with its final config/genomes
+        //    up front, then copy the base source's partition data into it ─────
         info!(
-            "bootstrap: copying {} → {} ({} genome(s))",
-            sources[0].root_path.display(),
+            "bootstrap: {} → {} ({} genome(s))",
+            sources[0].dir().display(),
             output.display(),
             src_genomes[0].len(),
         );
         let t = Stage::start("bootstrap");
-        let pb = spinner("bootstrap");
-        pb.set_message("copying index …");
-        copy_dir_all(&sources[0].root_path, output)?;
 
-        let dst_meta = IndexMeta::open_at(output).map_err(OKIError::Io)?;
-        let mut config = dst_meta.config.clone();
-        config.with_counts = mode == MergeMode::Count;
+        let mut config = sources[0].meta().config.clone();
+        config.with_counts = self.mode == MergeMode::Count;
         config.evidence = evidence.clone();
-        dst_meta.rewrite_config(config, all_genomes).map_err(OKIError::Io)?;
 
-        if mode == MergeMode::Presence {
-            remove_dirs_named(output, "counts")?;
+        let dst = KmerIndex::create(&output, config, None)?;
+        dst.meta()
+            .set_genomes(all_genomes)
+            .map_err(|e| io::Error::other(e.to_string()))?;
+
+        copy_dir_all(
+            &sources[0].dir().join(PARTITIONS_SUBDIR),
+            &output.join(PARTITIONS_SUBDIR),
+        )?;
+
+        if self.mode == MergeMode::Presence {
+            remove_dirs_named(&output, "counts")?;
         }
-        pb.finish_and_clear();
-        rep.push(t.stop());
+        self.reporter.push(t.stop());
 
         // ── Rebuild spectrums ─────────────────────────────────────────────────
         info!("rebuilding spectrums for {} source(s)", sources.len());
         let t = Stage::start("spectrums");
-        let pb = spinner("spectrums");
-        pb.set_message("copying …");
         let spectrums_dir = output.join("spectrums");
         if spectrums_dir.exists() {
             fs::remove_dir_all(&spectrums_dir)?;
         }
         for ((src, new_labels), genomes) in sources.iter().zip(&source_labels).zip(&src_genomes) {
             let old_labels: Vec<String> = genomes.iter().map(|g| g.label.clone()).collect();
-            copy_spectrums(&src.root_path, output, &old_labels, new_labels)?;
+            copy_spectrums(src.dir(), &output, &old_labels, new_labels)?;
         }
-        pb.finish_and_clear();
-        rep.push(t.stop());
+        self.reporter.push(t.stop());
 
-        // ── Open destination ──────────────────────────────────────────────────
-        let dst = KmerIndex::open(output)?;
         let n_partitions = dst.n_partitions();
         let n_dst_genomes = src_genomes[0].len();
 
@@ -199,11 +257,9 @@ impl KmerIndex {
                 n_partitions, n_src_genomes, n_dst_genomes,
             );
             let t = Stage::start("merge_partitions");
-            let pb = progress_bar("merge", n_partitions as u64, "partitions");
 
-            let block_bits = dst.meta.config.block_bits;
+            let block_bits = dst.meta().config.block_bits;
 
-            // Pre-build source list once (avoid rebuilding per partition)
             let srcs: Vec<(&KmerIndex, usize)> = remaining_sources
                 .iter()
                 .zip(&src_genomes[1..])
@@ -224,30 +280,27 @@ impl KmerIndex {
             let mut order: Vec<usize> = (0..n_partitions).collect();
             order.sort_unstable_by_key(|&i| std::cmp::Reverse(partition_sizes[i]));
 
-            let _ = budget_fraction; // kept in signature for CLI compatibility
-
-            // Shadow as references so closures can capture them by copy.
             let srcs = &srcs;
             let evidence = &evidence;
+            let mode = self.mode;
 
             let runner = PartitionRunner::new();
             let mut part_stats: Vec<PartStat> = Vec::with_capacity(n_partitions);
+            let mut done: u64 = 0;
+            let on_progress = &mut self.on_progress;
 
             runner
                 .run(
                     &order,
-                    |i| {
-                        dst.merge_partition(
-                            i,
-                            srcs,
-                            mode,
-                            n_dst_genomes,
-                            block_bits,
-                            evidence,
-                        )
-                    },
+                    |i| merge_partition(&dst, i, srcs, mode, n_dst_genomes, block_bits, evidence),
                     |i, g_len, dur| {
-                        pb.inc(1);
+                        done += 1;
+                        if let Some(cb) = on_progress.as_mut() {
+                            cb(Progress {
+                                position: done,
+                                total: Some(n_partitions as u64),
+                            });
+                        }
                         debug!(
                             "partition {i}: done in {:.1}s — {} new kmers",
                             dur.as_secs_f64(),
@@ -260,29 +313,19 @@ impl KmerIndex {
                         });
                     },
                 )
-                .map_err(OKIError::Partition)?;
+                .map_err(|e| io::Error::other(e.to_string()))?;
 
-            pb.finish_and_clear();
-
-            // ── Diagnostic report ─────────────────────────────────────────────
             print_merge_partition_report(&part_stats, runner.max_workers());
 
-            rep.push(t.stop());
+            self.reporter.push(t.stop());
         }
 
-        // ── Pack matrices after merge ─────────────────────────────────────────
-        {
-            let t = Stage::start("pack");
-            let pb = spinner("pack");
-            pb.set_message("consolidating column files …");
-            let dst2 = KmerIndex::open(output)?;
-            dst2.pack_matrices(false)?;
-            dst2.meta.mark_indexed().map_err(OKIError::Io)?;
-            pb.finish_and_clear();
-            rep.push(t.stop());
-        }
+        // ── Finalize: pack matrices, mark indexed, reopen ──────────────────────
+        let t = Stage::start("finalize");
+        let dst = KmerIndex::finalize_indexed(&output, &mut self.reporter)?;
+        self.reporter.push(t.stop());
 
-        KmerIndex::open(output)
+        Ok(dst)
     }
 }
 
@@ -339,7 +382,9 @@ fn fmt_bytes(b: u64) -> String {
 fn partition_unitig_bytes(src: &KmerIndex, i: usize) -> u64 {
     let mut total = 0u64;
     for l in 0.. {
-        let p = src.layer_unitigs_path(i, l);
+        let Ok(p) = src.layer_unitigs_path(i, l) else {
+            break;
+        };
         if !p.exists() {
             break;
         }
@@ -353,7 +398,7 @@ fn partition_unitig_bytes(src: &KmerIndex, i: usize) -> u64 {
 fn compute_labels(
     src_genomes: &[Vec<GenomeInfo>],
     rename_duplicates: bool,
-) -> OKIResult<(Vec<Vec<String>>, Vec<GenomeInfo>)> {
+) -> io::Result<(Vec<Vec<String>>, Vec<GenomeInfo>)> {
     let mut seen: HashMap<String, usize> = HashMap::new();
     let mut source_labels: Vec<Vec<String>> = Vec::with_capacity(src_genomes.len());
     let mut all_genomes: Vec<GenomeInfo> = Vec::new();
@@ -368,7 +413,10 @@ fn compute_labels(
             } else if rename_duplicates {
                 format!("{label}.{count}")
             } else {
-                return Err(OKIError::DuplicateGenomeLabel(label.clone()));
+                return Err(io::Error::new(
+                    io::ErrorKind::AlreadyExists,
+                    format!("duplicate genome label: {label}"),
+                ));
             };
             *count += 1;
             labels.push(new_label.clone());
@@ -437,7 +485,7 @@ fn choose_base(sources: &[&KmerIndex], src_genomes: &[Vec<GenomeInfo>], mode: Me
     let needs_approx = sources.iter().enumerate().any(|(i, src)| {
         !is_trivial(&src_genomes[i], mode)
             && matches!(
-                src.meta.config.evidence,
+                src.meta().config.evidence,
                 IndexMode::Approx { .. } | IndexMode::Hybrid { .. }
             )
     });
@@ -448,7 +496,7 @@ fn choose_base(sources: &[&KmerIndex], src_genomes: &[Vec<GenomeInfo>], mode: Me
         .filter(|(_, src)| {
             !needs_approx
                 || matches!(
-                    src.meta.config.evidence,
+                    src.meta().config.evidence,
                     IndexMode::Approx { .. } | IndexMode::Hybrid { .. }
                 )
         })
diff --git a/src/obikmerge/src/partition_merge.rs b/src/obikmerge/src/partition_merge.rs
new file mode 100644
index 00000000..55de21eb
--- /dev/null
+++ b/src/obikmerge/src/partition_merge.rs
@@ -0,0 +1,645 @@
+//! Merging a source partition's new layer into a destination partition's
+//! de Bruijn graph union (pass 1) then column fill (pass 2). Free function,
+//! not a `KmerIndex` method — `KmerIndex` stays the stateless
+//! `Index { Partition { Layer } }` data model; this is one of the
+//! algorithms that reads/writes through it, living here in `obikmerge`
+//! instead.
+
+use std::fs;
+use std::io;
+use std::path::{Path, PathBuf};
+use std::sync::{Arc, Mutex};
+
+use obipipeline::{
+    Pipeline, PipelineError, PipelineSender, SharedFlatFn, Stage, ThrottleGuard, WorkerPool,
+    make_sink, make_source, make_transform, throttle,
+};
+use tracing::debug;
+
+use obicompactvec::{PersistentBitMatrixBuilder, PersistentCompactIntMatrixBuilder};
+use obikindex::layer::{IndexMode, KmerLayer, TypedLayer};
+use obikindex::{ColBuilder, KmerIndex, OKIError, OKIResult};
+use obikindexer::{build_graph, materialize_layer};
+use obikseq::CanonicalKmer;
+use obiskio::UnitigFileReader;
+
+use crate::MergeMode;
+
+// ── MatrixBuilder ─────────────────────────────────────────────────────────────
+//
+// Wraps whichever matrix builder `mode` calls for, so the merge pipeline never
+// has to know the on-disk column naming (`col_NNNNNN.pbiv`/`.pciv`) or the
+// matrix `meta.json` schema itself — both stay private to obicompactvec.
+// `resume` reopens a matrix directory already closed by a previous builder
+// session (an existing destination layer), continuing from its current
+// `n_cols` instead of starting a fresh matrix at 0.
+
+enum MatrixBuilder {
+    Bit(PersistentBitMatrixBuilder),
+    Int(PersistentCompactIntMatrixBuilder),
+}
+
+impl MatrixBuilder {
+    fn new(mode: MergeMode, n: usize, dir: &Path) -> io::Result<Self> {
+        Ok(match mode {
+            MergeMode::Presence => MatrixBuilder::Bit(PersistentBitMatrixBuilder::new(n, dir)?),
+            MergeMode::Count => MatrixBuilder::Int(PersistentCompactIntMatrixBuilder::new(n, dir)?),
+        })
+    }
+
+    fn resume(mode: MergeMode, dir: &Path) -> io::Result<Self> {
+        Ok(match mode {
+            MergeMode::Presence => MatrixBuilder::Bit(PersistentBitMatrixBuilder::resume(dir)?),
+            MergeMode::Count => MatrixBuilder::Int(PersistentCompactIntMatrixBuilder::resume(dir)?),
+        })
+    }
+
+    /// Add a column with no data written (all-zero/false) — for genome
+    /// columns absent from this source (e.g. dst genomes in a new layer).
+    fn add_absent_col(&mut self) -> io::Result<()> {
+        match self {
+            MatrixBuilder::Bit(b) => b.add_col()?.close(),
+            MatrixBuilder::Int(b) => b.add_col()?.close(),
+        }
+    }
+
+    fn add_col(&mut self) -> io::Result<ColBuilder> {
+        Ok(match self {
+            MatrixBuilder::Bit(b) => ColBuilder::Bit(b.add_col()?),
+            MatrixBuilder::Int(b) => ColBuilder::Int(b.add_col()?),
+        })
+    }
+
+    fn close(self) -> io::Result<()> {
+        match self {
+            MatrixBuilder::Bit(b) => b.close(),
+            MatrixBuilder::Int(b) => b.close(),
+        }
+    }
+}
+
+#[cfg(test)]
+mod matrix_builder_tests {
+    use tempfile::tempdir;
+
+    use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+
+    use super::{ColBuilder, MatrixBuilder, MergeMode};
+
+    /// Mirrors `merge_partition`'s "new layer" setup: absent (dst-genome)
+    /// columns get no data, then source columns are filled — all through one
+    /// continuous `MatrixBuilder` session, closed once at the end.
+    #[test]
+    fn new_layer_absent_then_source_columns_presence() {
+        let dir = tempdir().unwrap();
+        let data_dir = dir.path().join("presence");
+        let mut mb = MatrixBuilder::new(MergeMode::Presence, 3, &data_dir).unwrap();
+
+        // Two absent (dst-genome) columns.
+        mb.add_absent_col().unwrap();
+        mb.add_absent_col().unwrap();
+
+        // One source column, filled like pass 2 would.
+        let mut col = mb.add_col().unwrap();
+        match &mut col {
+            ColBuilder::Bit(b) => {
+                b.set(0, true);
+                b.set(1, false);
+                b.set(2, true);
+            }
+            ColBuilder::Int(_) => unreachable!(),
+        }
+        col.close().unwrap();
+        mb.close().unwrap();
+
+        let m = PersistentBitMatrix::open(dir.path()).unwrap();
+        assert_eq!(m.n_cols(), 3);
+        assert_eq!(&*m.row(0), &[false, false, true]);
+        assert_eq!(&*m.row(1), &[false, false, false]);
+        assert_eq!(&*m.row(2), &[false, false, true]);
+    }
+
+    #[test]
+    fn new_layer_absent_then_source_columns_count() {
+        let dir = tempdir().unwrap();
+        let data_dir = dir.path().join("counts");
+        let mut mb = MatrixBuilder::new(MergeMode::Count, 2, &data_dir).unwrap();
+
+        mb.add_absent_col().unwrap();
+
+        let mut col = mb.add_col().unwrap();
+        match &mut col {
+            ColBuilder::Int(b) => {
+                b.set(0, 7);
+                b.set(1, 42);
+            }
+            ColBuilder::Bit(_) => unreachable!(),
+        }
+        col.close().unwrap();
+        mb.close().unwrap();
+
+        let m = PersistentCompactIntMatrix::open(dir.path()).unwrap();
+        assert_eq!(m.n_cols(), 2);
+        assert_eq!(&*m.row(0), &[0u32, 7]);
+        assert_eq!(&*m.row(1), &[0u32, 42]);
+    }
+
+    /// Mirrors `merge_partition`'s "existing dst layer" setup: an
+    /// already-closed matrix (from a previous merge) gets more columns
+    /// appended via `resume`, without callers ever seeing `col_path`/
+    /// `MatrixMeta` — `n` itself is read back from the matrix directory.
+    #[test]
+    fn resume_appends_source_columns_to_existing_layer() {
+        let dir = tempdir().unwrap();
+        let data_dir = dir.path().join("presence");
+
+        // Previous merge: one dst-genome column already on disk.
+        let mut mb0 = MatrixBuilder::new(MergeMode::Presence, 3, &data_dir).unwrap();
+        mb0.add_absent_col().unwrap();
+        mb0.close().unwrap();
+
+        // This merge: resume and append two more source columns.
+        let mut mb = MatrixBuilder::resume(MergeMode::Presence, &data_dir).unwrap();
+        for vals in [[true, false, true], [false, true, false]] {
+            let mut col = mb.add_col().unwrap();
+            match &mut col {
+                ColBuilder::Bit(b) => {
+                    for (slot, v) in vals.into_iter().enumerate() {
+                        b.set(slot, v);
+                    }
+                }
+                ColBuilder::Int(_) => unreachable!(),
+            }
+            col.close().unwrap();
+        }
+        mb.close().unwrap();
+
+        let m = PersistentBitMatrix::open(dir.path()).unwrap();
+        assert_eq!(m.n_cols(), 3);
+        assert_eq!(&*m.row(0), &[false, true, false]);
+        assert_eq!(&*m.row(1), &[false, false, true]);
+        assert_eq!(&*m.row(2), &[false, true, false]);
+    }
+}
+
+// ── dst cross-layer lookup ──────────────────────────────────────────────────
+
+/// Batch membership lookup across `dst_layers` — first layer that carries
+/// each kmer wins. Groups hits by layer index (as `(kmer batch index,
+/// slot)` pairs) rather than returning them in query order, so pass 2 can
+/// follow with one column-major write per `(layer, column)` instead of
+/// interleaving across layers kmer by kmer. The kmers with no hit in any
+/// layer come back as a separate index list, for the new-layer MPHF batch
+/// lookup on a miss.
+fn find_batch_grouped(
+    layers: &[KmerLayer],
+    kmers: &[CanonicalKmer],
+) -> (Vec<Vec<(usize, usize)>>, Vec<usize>) {
+    let mut by_layer: Vec<Vec<(usize, usize)>> = vec![Vec::new(); layers.len()];
+    let mut not_found: Vec<usize> = Vec::new();
+    for (idx, &kmer) in kmers.iter().enumerate() {
+        match layers
+            .iter()
+            .enumerate()
+            .find_map(|(li, l)| l.find_slot(kmer).map(|slot| (li, slot)))
+        {
+            Some((li, slot)) => by_layer[li].push((idx, slot)),
+            None => not_found.push(idx),
+        }
+    }
+    (by_layer, not_found)
+}
+
+// ── merge_partition ────────────────────────────────────────────────────────
+
+/// Merge `sources` into destination partition `i`.
+///
+/// Each entry in `sources` is `(index, n_genomes)` where `n_genomes` is the
+/// number of genome columns that source contributes. A merged index
+/// contributes more than one. The total new columns added to the
+/// destination is `sum(n_genomes)`.
+///
+/// `n_dst_genomes` is the number of genome columns already in the
+/// destination matrices (copied from the bootstrap source before this
+/// call).
+pub(crate) fn merge_partition(
+    dst: &KmerIndex,
+    i: usize,
+    sources: &[(&KmerIndex, usize)],
+    mode: MergeMode,
+    n_dst_genomes: usize,
+    block_bits: u8,
+    evidence: &IndexMode,
+) -> OKIResult<usize> {
+    let dst_partition = dst.partition(i)?;
+    let n_dst_layers = dst_partition.n_layers();
+    let n_src_total: usize = sources.iter().map(|(_, n)| *n).sum();
+
+    // First merge in presence mode: materialize implicit single-genome
+    // presence matrices on existing layers (all slots true — every kmer in
+    // those layers belongs to genome_0) so a resumed builder can append
+    // source columns onto them below.
+    if n_dst_genomes == 1 && mode == MergeMode::Presence {
+        for l in 0..n_dst_layers {
+            let layer = dst_partition.layer(l)?.open()?;
+            TypedLayer::<()>::init_presence_matrix(layer.dir(), layer.n())?;
+        }
+    }
+
+    // dst's `0..n_dst_layers` layers and every source's own layers, for
+    // this one partition — all opened the same direct way, not via
+    // `IndexCache`. Every layer read here (dst's pre-existing ones, and
+    // every source's) is just as stable for the duration of this call: dst
+    // only ever gets a brand new layer *appended* below, never one of these
+    // read from, so there's no "dst isn't stable" distinction between the
+    // two loops — `IndexCache` still doesn't fit either one, for a single,
+    // uniform reason: `obikindexer::build_graph`/`obipipeline::WorkerPool`
+    // (pass 1/2 below) are plain-OS-thread pipelines requiring `Send + Sync
+    // + 'static`, and `IndexCache<'_>` always borrows `&KmerIndex` — no
+    // amount of logical stability changes that a borrowed cache can't cross
+    // that boundary, only owned `KmerLayer`s can (each owns its own mmap'd
+    // files, no reference back to the index it came from).
+    let dst_layers: Vec<KmerLayer> = (0..n_dst_layers)
+        .map(|l| dst_partition.layer(l)?.open())
+        .collect::<OKIResult<_>>()?;
+    let dst_layers = Arc::new(dst_layers);
+
+    let src_layers: Vec<Vec<Arc<KmerLayer>>> = sources
+        .iter()
+        .map(|(src, _)| -> OKIResult<Vec<Arc<KmerLayer>>> {
+            let partition = src.partition(i)?;
+            (0..partition.n_layers())
+                .map(|l| partition.layer(l)?.open().map(Arc::new))
+                .collect()
+        })
+        .collect::<OKIResult<_>>()?;
+
+    // ── Pass 1: pipeline — parallel file read + dst filter + graph fill ────
+    //
+    // Source  : list of unitigs.bin paths (one per source × layer)
+    // Flat    : open file, emit Vec<CanonicalKmer> batches (BeeGFS parallel I/O)
+    // Transform: filter via dst_layers — Arc<[KmerLayer]>: Sync
+    // Sink    : push new kmers into GraphDeBruijn (single thread, no locks needed)
+
+    let mut unitig_paths: Vec<PathBuf> = Vec::new();
+    for layers in &src_layers {
+        for layer in layers {
+            let p = layer.unitigs_path();
+            if p.exists() {
+                unitig_paths.push(p);
+            }
+        }
+    }
+
+    let n_src_layers = unitig_paths.len();
+    debug!("partition {i}: de Bruijn graph build start — {n_src_layers} source layer(s)");
+
+    const BATCH: usize = 4096;
+    let n_workers = rayon::current_num_threads().min(16).max(4);
+    // At most 2 files open simultaneously: keeps n_workers-2 workers free
+    // for the Transform stage. Each open file monopolises one worker for the
+    // full duration of its read, so this must stay well below n_workers.
+    let max_open = 2;
+
+    let dst_filter = Arc::clone(&dst_layers);
+
+    let g = build_graph(
+        unitig_paths.into_iter(),
+        move |path: PathBuf, emit: &mut dyn FnMut(Vec<CanonicalKmer>)| -> OKIResult<()> {
+            let reader = UnitigFileReader::open_sequential(&path)?;
+            let mut batch: Vec<CanonicalKmer> = Vec::with_capacity(BATCH);
+            for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                batch.push(kmer);
+                if batch.len() == BATCH {
+                    emit(std::mem::replace(&mut batch, Vec::with_capacity(BATCH)));
+                }
+            }
+            if !batch.is_empty() {
+                emit(batch);
+            }
+            Ok(())
+        },
+        move |kmer| dst_filter.iter().all(|l| l.find_slot(kmer).is_none()),
+        n_workers,
+        max_open,
+    )?;
+
+    let any_new = g.len() > 0;
+    debug!(
+        "partition {i}: de Bruijn graph done — {} new kmers",
+        g.len()
+    );
+
+    // Build new layer from de Bruijn graph if there are new kmers.
+    let new_layer_idx = n_dst_layers;
+    let new_layer_dir = KmerLayer::new(&dst_partition, new_layer_idx)
+        .dir()
+        .to_path_buf();
+
+    let n_new = if any_new {
+        debug!("partition {i}: unitig traversal start — {} nodes", g.len());
+        let n_nodes = materialize_layer(g, &new_layer_dir, block_bits, evidence)?;
+        debug!("partition {i}: MPHF build done");
+        n_nodes
+    } else {
+        drop(g);
+        0
+    };
+
+    let t_open = std::time::Instant::now();
+    let new_mphf: Option<Arc<obikindex::layer::MphfOnly>> = if any_new {
+        Some(Arc::new(obikindex::layer::MphfOnly::open(&new_layer_dir)?))
+    } else {
+        None
+    };
+    debug!(
+        "partition {i}: MPHF open in {:.3}s",
+        t_open.elapsed().as_secs_f64()
+    );
+
+    // ── Prepare matrix directories for the new layer ──────────────────────
+    // Absent columns (dst genomes) get an all-zero/false column. Source-genome
+    // columns are created as mutable builders for pass 2. `new_mb` is kept
+    // open (not `close`d) until pass 2 has filled every source column, so its
+    // `n_cols` bookkeeping stays in sync with the columns actually created.
+    let (new_src_builders, new_mb): (Vec<ColBuilder>, Option<MatrixBuilder>) = if any_new {
+        let data_dir = match mode {
+            MergeMode::Presence => new_layer_dir.join("presence"),
+            MergeMode::Count => new_layer_dir.join("counts"),
+        };
+        fs::create_dir_all(&data_dir)?;
+        let mut mb = MatrixBuilder::new(mode, n_new, &data_dir).map_err(OKIError::Io)?;
+        for _ in 0..n_dst_genomes {
+            mb.add_absent_col().map_err(OKIError::Io)?;
+        }
+        let cols = (0..n_src_total)
+            .map(|_| mb.add_col().map_err(OKIError::Io))
+            .collect::<OKIResult<Vec<_>>>()?;
+        (cols, Some(mb))
+    } else {
+        (vec![], None)
+    };
+
+    let t_builders = std::time::Instant::now();
+    // Builders for existing layers: n_src_total per layer, resumed from
+    // each layer's own matrix directory (already holding n_dst_genomes
+    // columns from a previous merge). Columns land at
+    // n_dst_genomes .. n_dst_genomes + n_src_total - 1.
+    let mut exist_mbs: Vec<MatrixBuilder> = Vec::with_capacity(n_dst_layers);
+    let mut exist_builders: Vec<Vec<ColBuilder>> = Vec::with_capacity(n_dst_layers);
+    for l in 0..n_dst_layers {
+        let layer_dir = dst_layers[l].dir().to_path_buf();
+        let data_dir = match mode {
+            MergeMode::Presence => layer_dir.join("presence"),
+            MergeMode::Count => layer_dir.join("counts"),
+        };
+        let mut mb = MatrixBuilder::resume(mode, &data_dir).map_err(OKIError::Io)?;
+        let cols = (0..n_src_total)
+            .map(|_| mb.add_col().map_err(OKIError::Io))
+            .collect::<OKIResult<Vec<_>>>()?;
+        exist_mbs.push(mb);
+        exist_builders.push(cols);
+    }
+
+    debug!(
+        "partition {i}: builders ready in {:.3}s",
+        t_builders.elapsed().as_secs_f64()
+    );
+
+    // ── Pass 2: fill builders (pipeline) ─────────────────────────────────
+    let t_pass2 = std::time::Instant::now();
+    // Collect source items before the pipeline so errors propagate via ?
+    // before any worker thread is spawned.
+    let mut pass2_items: Vec<(usize, usize, PathBuf, Arc<KmerLayer>)> = Vec::new();
+    {
+        let mut col_offset = 0usize;
+        for ((_, src_n), layers) in sources.iter().zip(src_layers.iter()) {
+            for layer in layers {
+                let unitigs_path = layer.unitigs_path();
+                if unitigs_path.exists() {
+                    pass2_items.push((col_offset, *src_n, unitigs_path, Arc::clone(layer)));
+                }
+            }
+            col_offset += src_n;
+        }
+    }
+
+    enum Pass2Data {
+        SrcLayer((usize, usize, PathBuf, Arc<KmerLayer>, ThrottleGuard)),
+        RawBatch((usize, usize, Arc<KmerLayer>, Vec<CanonicalKmer>)),
+        /// One entry per `(dst layer, absolute column)` touched by this
+        /// batch, each carrying every `(slot, value)` pair for that column
+        /// together — column-major, so the sink below locks that column's
+        /// `ColBuilder` once per batch and writes the whole run, instead of
+        /// once per `(kmer, genome)` pair.
+        WriteBatch(Vec<(Option<usize>, usize, Vec<(usize, u32)>)>),
+    }
+
+    let exist_locked: Vec<Vec<Arc<Mutex<ColBuilder>>>> = exist_builders
+        .into_iter()
+        .map(|layer| layer.into_iter().map(|b| Arc::new(Mutex::new(b))).collect())
+        .collect();
+    let new_locked: Vec<Arc<Mutex<ColBuilder>>> = new_src_builders
+        .into_iter()
+        .map(|b| Arc::new(Mutex::new(b)))
+        .collect();
+    let exist_sink: Vec<Vec<Arc<Mutex<ColBuilder>>>> = exist_locked
+        .iter()
+        .map(|layer| layer.iter().map(Arc::clone).collect())
+        .collect();
+    let new_sink: Vec<Arc<Mutex<ColBuilder>>> = new_locked.iter().map(Arc::clone).collect();
+    let dst_layers_t2 = Arc::clone(&dst_layers);
+    let new_mphf_t2 = new_mphf.clone();
+    let pass2_err: Arc<Mutex<Option<String>>> = Arc::new(Mutex::new(None));
+    let err_cap2 = Arc::clone(&pass2_err);
+
+    let capacity = 2;
+    let throttled_pass2 = throttle(pass2_items.into_iter(), max_open);
+
+    let pipeline2 = Pipeline::new(
+        make_source!(
+            Pass2Data,
+            throttled_pass2.map(|t| {
+                let (col_offset, src_n, unitigs_path, src_layer) = t.item;
+                (col_offset, src_n, unitigs_path, src_layer, t.guard)
+            }),
+            SrcLayer
+        ),
+        vec![
+            Stage::Flat(Arc::new(
+                move |data: Pass2Data,
+                      push: &PipelineSender<Result<Pass2Data, PipelineError>>,
+                      delta: &PipelineSender<isize>| {
+                    if let Pass2Data::SrcLayer((col_offset, src_n, unitigs_path, src_layer, _guard)) =
+                        data
+                    {
+                        // _guard dropped at end of block, releasing the slot.
+                        // `src_layer` (MPHF + matrix) was already opened up
+                        // front — only the unitigs.bin stream itself is
+                        // opened (and throttled) here.
+                        let reader = match UnitigFileReader::open_sequential(&unitigs_path) {
+                            Ok(r) => r,
+                            Err(e) => {
+                                *err_cap2.lock().unwrap() = Some(e.to_string());
+                                delta.send(-1).ok();
+                                return;
+                            }
+                        };
+                        const BATCH: usize = 4096;
+                        let mut batch: Vec<CanonicalKmer> = Vec::with_capacity(BATCH);
+                        let mut count: isize = 0;
+                        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                            batch.push(kmer);
+                            if batch.len() == BATCH {
+                                let b = std::mem::replace(&mut batch, Vec::with_capacity(BATCH));
+                                push.send(Ok(Pass2Data::RawBatch((
+                                    col_offset,
+                                    src_n,
+                                    Arc::clone(&src_layer),
+                                    b,
+                                ))))
+                                .ok();
+                                count += 1;
+                            }
+                        }
+                        if !batch.is_empty() {
+                            push.send(Ok(Pass2Data::RawBatch((col_offset, src_n, src_layer, batch))))
+                                .ok();
+                            count += 1;
+                        }
+                        delta.send(count - 1).ok();
+                    }
+                },
+            ) as SharedFlatFn<Pass2Data>),
+            make_transform!(
+                Pass2Data,
+                {
+                    move |(col_offset, src_n, src_layer, kmers): (
+                        usize,
+                        usize,
+                        Arc<KmerLayer>,
+                        Vec<CanonicalKmer>,
+                    )|
+                          -> Vec<(Option<usize>, usize, Vec<(usize, u32)>)> {
+                        // Column-first, one pass for the whole batch: a single
+                        // MPHF hash sweep (`hash_batch`) instead of one hash
+                        // per kmer, then one read pass per source genome
+                        // column (`fill_sub_matrix`) instead of one row read
+                        // per kmer — matches the underlying matrix's own
+                        // column-major layout.
+                        let slots = src_layer.hash_batch(&kmers);
+                        let mut cols: Vec<Vec<u32>> =
+                            (0..src_n).map(|_| Vec::with_capacity(kmers.len())).collect();
+                        src_layer.fill_sub_matrix(&slots, &mut cols);
+
+                        // Membership against dst, grouped by dst layer
+                        // instead of interleaved kmer by kmer — same
+                        // grouping `PartitionCache::find_presence_batch`
+                        // does in `obikphylo`, via the shared primitive.
+                        let (by_dst_layer, not_found) = find_batch_grouped(&dst_layers_t2, &kmers);
+
+                        // Genome-major within each layer group (not kmer-major)
+                        // so every `(layer, col)` pair's values land together —
+                        // one entry per column, not one per `(kmer, genome)`.
+                        let mut ops: Vec<(Option<usize>, usize, Vec<(usize, u32)>)> =
+                            Vec::with_capacity(src_n * (by_dst_layer.len() + 1));
+                        for (dst_layer, hits) in by_dst_layer.into_iter().enumerate() {
+                            if hits.is_empty() {
+                                continue;
+                            }
+                            for g in 0..src_n {
+                                let col_vals: Vec<(usize, u32)> = hits
+                                    .iter()
+                                    .map(|&(idx, slot)| (slot, cols[g][idx]))
+                                    .collect();
+                                ops.push((Some(dst_layer), col_offset + g, col_vals));
+                            }
+                        }
+                        if let (Some(mphf), false) = (&new_mphf_t2, not_found.is_empty()) {
+                            let not_found_kmers: Vec<CanonicalKmer> =
+                                not_found.iter().map(|&idx| kmers[idx]).collect();
+                            let new_slots = mphf.index_batch(&not_found_kmers);
+                            for g in 0..src_n {
+                                let col_vals: Vec<(usize, u32)> = not_found
+                                    .iter()
+                                    .zip(new_slots.iter())
+                                    .map(|(&idx, &slot)| (slot, cols[g][idx]))
+                                    .collect();
+                                ops.push((None, col_offset + g, col_vals));
+                            }
+                        }
+                        ops
+                    }
+                },
+                RawBatch,
+                WriteBatch
+            ),
+        ],
+        make_sink!(
+            Pass2Data,
+            {
+                move |ops: Vec<(Option<usize>, usize, Vec<(usize, u32)>)>| {
+                    for (layer_opt, col, col_vals) in ops {
+                        let builder = match layer_opt {
+                            Some(l) => &exist_sink[l][col],
+                            None => &new_sink[col],
+                        };
+                        let mut b = builder.lock().unwrap();
+                        for (slot, val) in col_vals {
+                            b.set_val(slot, val);
+                        }
+                    }
+                }
+            },
+            WriteBatch
+        ),
+    );
+
+    WorkerPool::new(pipeline2, n_workers, capacity).run();
+    debug!(
+        "partition {i}: pass2 pipeline done in {:.3}s",
+        t_pass2.elapsed().as_secs_f64()
+    );
+
+    if let Some(msg) = Arc::try_unwrap(pass2_err)
+        .unwrap_or_else(|_| panic!("pass2: pass2_err not uniquely owned"))
+        .into_inner()
+        .unwrap_or_else(|e| e.into_inner())
+    {
+        return Err(OKIError::InvalidData {
+            context: "merge pass2",
+            detail: msg,
+        });
+    }
+
+    let t_close = std::time::Instant::now();
+    // ── Close builders ──────────────────────────────────────────────────
+    for (mb, builders) in exist_mbs.into_iter().zip(exist_locked.into_iter()) {
+        for b in builders {
+            Arc::try_unwrap(b)
+                .unwrap_or_else(|_| panic!("pass2: exist_builder not uniquely owned"))
+                .into_inner()
+                .unwrap_or_else(|e| e.into_inner())
+                .close()?;
+        }
+        mb.close().map_err(OKIError::Io)?;
+    }
+
+    for b in new_locked {
+        Arc::try_unwrap(b)
+            .unwrap_or_else(|_| panic!("pass2: new_builder not uniquely owned"))
+            .into_inner()
+            .unwrap_or_else(|e| e.into_inner())
+            .close()?;
+    }
+    if let Some(mb) = new_mb {
+        mb.close().map_err(OKIError::Io)?;
+    }
+
+    debug!(
+        "partition {i}: builders closed in {:.3}s",
+        t_close.elapsed().as_secs_f64()
+    );
+
+    Ok(n_new)
+}