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< h1 id = "obikmer" > obikmer</ h1 >
< p >< code > obikmer</ code > is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.</ p >
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< h2 id = "subcommands" > Subcommands</ h2 >
< table >
< thead >
< tr >
< th > Subcommand</ th >
< th > Purpose</ th >
</ tr >
</ thead >
< tbody >
< tr >
< td >< code > superkmer</ code ></ td >
< td > Extract super-kmers from a sequence file and write to stdout</ td >
</ tr >
< tr >
< td >< code > index</ code ></ td >
< td > Build a complete genome index (scatter → dereplicate → count → layered MPHF)</ td >
</ tr >
< tr >
< td >< code > merge</ code ></ td >
< td > Merge multiple built indexes into one</ td >
</ tr >
< tr >
< td >< code > rebuild</ code ></ td >
< td > Filter and compact an existing index into a new single-layer index; supports ingroup/outgroup predicates on genome metadata</ td >
</ tr >
< tr >
< td >< code > query</ code ></ td >
< td > Query an index with sequences and annotate matches</ td >
</ tr >
< tr >
< td >< code > dump</ code ></ td >
< td > Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the same ingroup/outgroup filtering as < code > rebuild</ code ></ td >
</ tr >
< tr >
< td >< code > annotate</ code ></ td >
< td > Add or update genome metadata from a CSV file; or dump metadata as CSV</ td >
</ tr >
< tr >
< td >< code > distance</ code ></ td >
< td > Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees</ td >
</ tr >
< tr >
< td >< code > unitig</ code ></ td >
< td > Build a global de Bruijn graph across all partitions and enumerate its unitigs as FASTA; supports the same ingroup/outgroup filtering as < code > rebuild</ code ></ td >
</ tr >
< tr >
< td >< code > estimate</ code ></ td >
< td > Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing</ td >
</ tr >
< tr >
< td >< code > reindex</ code ></ td >
< td > Convert an index's evidence in-place: exact ↔ approx</ td >
</ tr >
< tr >
< td >< code > utils</ code ></ td >
< td > Miscellaneous index utilities: < code > --new-label NEW=OLD</ code > renames a genome label; < code > --upgrade-index</ code > adds missing < code > layer_meta.json</ code > to old indexes</ td >
</ tr >
< tr >
< td >< code > pack</ code ></ td >
< td > Pack per-column matrix files into single-file format to reduce query I/O</ td >
</ tr >
</ tbody >
</ table >
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< h2 id = "constraints" > Constraints</ h2 >
< ul >
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< li > Target scale: individual genome datasets, tens of Gbases</ li >
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< li > Maximum efficiency in computation, memory, and disk usage</ li >
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< li > k odd, k ∈ [11, 31], fixed at runtime; kmer fits in a u64 (2 bits/base)</ li >
< li > Canonical form: < code > min(kmer, revcomp(kmer))</ code > reduces strand-symmetric space by half</ li >
< li > Input formats for < code > index</ code > /< code > superkmer</ code > : FASTA (< code > .fa</ code > , < code > .fasta</ code > ), FASTQ (< code > .fq</ code > , < code > .fastq</ code > ), GenBank flat file (< code > .gb</ code > , < code > .gbk</ code > , < code > .gbff</ code > ), all optionally gzip-compressed; directories expanded recursively; streaming stdin via < code > -</ code ></ li >
< li > Input formats for < code > query</ code > : FASTA, FASTQ, optionally gzip-compressed; streaming stdin via < code > -</ code ></ li >
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</ ul >
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< h2 id = "parameter-constraints-enforced-at-cli" > Parameter constraints (enforced at CLI)</ h2 >
< p > All constraints below are checked by < code > CommonArgs::validate()</ code > at the start of < code > superkmer</ code > and < code > index</ code > . Invalid values exit immediately with an error.</ p >
< table >
< thead >
< tr >
< th > Parameter</ th >
< th > Constraint</ th >
< th > Reason</ th >
</ tr >
</ thead >
< tbody >
< tr >
< td > k (< code > --kmer-size</ code > )</ td >
< td > odd</ td >
< td > even k allows palindromic k-mers: kmer == revcomp(kmer), breaking the canonical form invariant</ td >
</ tr >
< tr >
< td > k (< code > --kmer-size</ code > )</ td >
< td > k ∈ [11, 31]</ td >
< td > k > 31 overflows u64 at 2 bits/base; k < 11 gives insufficient specificity</ td >
</ tr >
< tr >
< td > m (< code > --minimizer-size</ code > )</ td >
< td > odd</ td >
< td > same palindrome argument as k</ td >
</ tr >
< tr >
< td > m (< code > --minimizer-size</ code > )</ td >
< td > 3 ≤ m ≤ k− </ td >
< td > minimizer must be strictly shorter than the kmer</ td >
</ tr >
< tr >
< td > z (< code > -z</ code > , Findere, < code > index --approx</ code > only)</ td >
< td > z ≤ k− </ td >
< td > effective indexed kmer size is k− </ td >
</ tr >
</ tbody >
</ table >
< h2 id = "genome-label-constraints" > Genome label constraints</ h2 >
< p > Genome labels are arbitrary Unicode strings with the following restrictions:</ p >
< table >
< thead >
< tr >
< th > Character</ th >
< th > Forbidden</ th >
< th > Reason</ th >
</ tr >
</ thead >
< tbody >
< tr >
< td >< code > /</ code ></ td >
< td > yes</ td >
< td > filesystem path separator</ td >
</ tr >
< tr >
< td >< code > =</ code ></ td >
< td > yes</ td >
< td >< code > --new-label</ code > parser separator</ td >
</ tr >
< tr >
< td >< code > \0</ code ></ td >
< td > yes</ td >
< td > null byte</ td >
</ tr >
< tr >
< td >< code > \n</ code > < code > \r</ code > < code > \t</ code ></ td >
< td > yes</ td >
< td > break CSV output</ td >
</ tr >
< tr >
< td > spaces</ td >
< td >< strong > allowed</ strong ></ td >
< td > use shell quoting: < code > --new-label 'new label=old label'</ code ></ td >
</ tr >
</ tbody >
</ table >
< p > Empty labels are also rejected. Labels derived automatically from the index directory name (when < code > --label</ code > is omitted) are not validated since they come from the filesystem and are already safe.</ p >
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< h2 id = "priority-operations" > Priority operations</ h2 >
< ul >
< li > Kmer counting (frequencies)</ li >
< li > Fast search / query</ li >
< li > Set operations: union, intersection, difference</ li >
</ ul >
</ article >
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