What Software Can Be Used To Attempt To Improve An Assembly By Filling Targeted Gaps Or Premature Contigs Endings?

Question

[JacobS]

I'm working on several rough genomes and am looking for ways to improve the assemblies. I have a linear genome, but it contains both gaps and missing sequence at the 5' and 3' end. I have a little bit of new sequence, and need a tool that will try to fill these gaps and extend the end of my linear genome. I've tried Gapfiller, which helped a little, but only for interior gaps and not exterior extension. Any thoughts?

[Joseph Hughes]

I've never tried this but can you pad your 5' and 3' sequence with Ns and then do a reference assembly. It could also be an issue with the way the library was prepared resulting in the lack of reads for the ends.

[JacobS]

Thanks for the input... As far as I can tell, adding N's to each end of my genome won't work with Gapfiller, which requires a read to stretch the gap being filled. Please correct me if I'm wrong. Do you know of any software that can do this?

[Phil S.]

Depending on your sequencing strategy this can be very useful: http://ccb.jhu.edu/software/FLASH/

Answer 1

[Rayan Chikhi]

Mapsembler 2 will show you what is at the 5' and 3' ends of your contigs, either in the form of a sequence, or if the extensions are ambiguous, it will show a graph of sequences.