Mapper to extned contigs

[dbrami]

Hello all,

Which mapping software would you use if you are looking to map reads back to a set of contigs, and most importantly, extend one contig into another if valid?

[SES]

With MIRA you can choose to build new contigs (abnc=yes) in combination with mapping if the reads don't fit in the reference. So, you are doing a de novo assembly in addition to mapping.

Not sure this is exactly what you want, but hope it helps.