Question

Does The Velvet Output Contig.Fa File Contain Both The Contig And Scaffolding Information?

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11.0 years ago

rob234king ▴ 610

Velvet produces various output files. Is the contigs.fa file both the scaffolding and contigs file? I want to separate files to compare with data from the GAGE study but don't know how to separate contigs from scaffold if in the same file? any help appreciated.

Rob

velvet scaffolding contigs • 4.3k views

ADD COMMENT • link 11.0 years ago by rob234king ▴ 610

score 2 · Answer 1 · 2013-04-09

contigs.fa is just sequences - the scaffolds will have NNN's in them but you shouldn't rely on that file to study an assembly. You really want to look at the velvet_asm.afg file, which is AMOS formatted. AMOS is pretty weird in that it uses the same vernacular to both describe nodes in a contig and contigs in a scaffold.

score 0 · Answer 2 · 2013-04-12

I have that file to look at but I want to run some statistics on the contigs and the assembly seperately as they did in the GAGE study however I'm unsure how to do that when its all contained in one file. I can do it using a seperate contig assembly file and a scaffold assembly file like from SOAP. The GAGE study doesn't say how they did that, I was hoping it was something obvious to produce a scaffolding file that isn't .afg that I can run some statistics on??

Thanks