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

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
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updated by Biostar Biostar • written by JacobS JacobS

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.

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written by Joseph Hughes Joseph Hughes

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?

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written by JacobS JacobS

1 answer

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.

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written by Rayan Chikhi Rayan Chikhi

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