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Old 03-07-2014, 08:15 AM   #7
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707


Sorry for the confusion. The files are called "chrom" for legacy reasons, and they don't correspond to chromosomes anymore. I should rename them "chunks". Originally, BBMap wrote one chromosome per chrom file, which is fine for complete reference genomes. But de-novo assemblies can have thousands or millions of scaffolds, so now I bundle them into chunks.

Everything is there, and when you produce a sam file, you'll see that reads are mapped to all of the different input chromosomes.
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