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docs: Update README to reflect new indexing workflow

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Replace the documented direct combined indexing command with a two-step workflow. This involves building separate exact indexes per genome, merging them into a single multi-genome index via `obikmer merge`, and keeping the approximate index conversion unchanged.
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Eric Coissac
2026-06-01 13:55:30 +02:00
parent 657f964dda
commit 1e2115a1b0
1 changed files with 6 additions and 3 deletions
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README.md
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@@ -79,9 +79,12 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats.
## Quick start ## Quick start
```sh ```sh
# Build an exact index for two genomes # Build an exact index for each genome independently
obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index/ obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index_a/
obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index/ obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index_b/
# Merge into a single multi-genome index
obikmer merge --output index/ index_a/ index_b/
# Convert to approximate index (z=5, 8-bit fingerprints) # Convert to approximate index (z=5, 8-bit fingerprints)
obikmer reindex --approx -z 5 --evidence-bits 8 index/ obikmer reindex --approx -z 5 --evidence-bits 8 index/