From 1e2115a1b082e398476e7df0500308d01b08a2a1 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 1 Jun 2026 13:55:30 +0200 Subject: [PATCH] docs: Update README to reflect new indexing workflow 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. --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1dc4d21..34d557a 100644 --- a/README.md +++ b/README.md @@ -79,9 +79,12 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats. ## Quick start ```sh -# Build an exact index for two genomes -obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index/ -obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index/ +# Build an exact index for each genome independently +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_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) obikmer reindex --approx -z 5 --evidence-bits 8 index/