Which Genome Assemblers Can Track The Reads In The Assembly Process?

Question

[2184687-1231-83-]

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?

Answer 1

[Eric Fournier]

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.

[Michael Schubert]

Velvet can do it as well.

[Bach]

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)