Question: Which Genome Assemblers Can Track The Reads In The Assembly Process?
3
gravatar for 2184687-1231-83-
8.9 years ago by
2184687-1231-83-5.0k wrote:

Which of the available genome assemblers can keep track of where each read is placed in the assembly process?
For those that do, what is the output format to point each read in the coordinates of the final set of contigs?

short assembly format tool • 1.2k views
ADD COMMENTlink modified 8.9 years ago by Eric Fournier1.4k • written 8.9 years ago by 2184687-1231-83-5.0k
3
gravatar for Eric Fournier
8.9 years ago by
Eric Fournier1.4k
Quebec, Canada
Eric Fournier1.4k wrote:

I do not have an extensive list, but I can tell you from experience that both CAP3 and MIRA do this. They can both produce .ace files, which detail the position of each read within the assembled contigs.

ADD COMMENTlink written 8.9 years ago by Eric Fournier1.4k

Velvet can do it as well.

ADD REPLYlink written 8.9 years ago by Michael Schubert6.9k

MIRA uses either the Sanger CAF, the ACE or the own MAF format to describe where each read is placed in the contig. Format definitions can be found at the Sanger Centre (CAF), in the ddocumentation of consed (ACE) or in the manual of MIRA (MAF)

ADD REPLYlink written 8.8 years ago by Bach550
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