Question: What Software Can Be Used To Attempt To Improve An Assembly By Filling Targeted Gaps Or Premature Contigs Endings?
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gravatar for JacobS
6.2 years ago by
JacobS900
Cleveland, Ohio
JacobS900 wrote:

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?

assembly ngs • 2.6k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 6.2 years ago by JacobS900

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.

ADD REPLYlink written 6.2 years ago by Joseph Hughes2.8k

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?

ADD REPLYlink written 6.2 years ago by JacobS900

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

ADD REPLYlink written 6.1 years ago by Phil S.660
0
gravatar for Rayan Chikhi
6.1 years ago by
Rayan Chikhi1.4k
France, Lille, CNRS
Rayan Chikhi1.4k wrote:

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.

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Rayan Chikhi1.4k
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