denovo on sam format

[bair]

Dear All,

I have alignment results in bam file which includes pair-end , mate-pair reads in different lengths, does anybody know Soap or other denovo program can handle bam file directly or I have to use the "raw" reads files? Can I mixture the reads in one file for denovo?

Many thanks!

[jmarshall]

Recent versions of Velvet can read directly from SAM and BAM files; it extracts qnames, pairing information, and sequence data, which is all it's interested in. The files must be sorted by (or at least grouped by) read name, but -- unlike other formats read by Velvet -- paired and unpaired reads can be mixed. See Daniel's announcement for details.

I don't know about other assemblers and SAM/BAM. You could of course use a tool like Picard's SamToFastq to reconstitute a more widely-read-by-assemblers format from your BAM files.

[bair]

Jmarshall, thank you very much.