Extend a contig using NGS library

Question

[drtamermansour]

Hi

Is there a tool I can use to extend a specific contig using a library of NGS data (it is PE library)?

Thank you

Answer 1

[Philipp Bayer]

I'd use SSPACE together with GapFiller (made by the same group). SSPACE scaffolds similar contigs using PE data, GapFiller then tries to fill the gaps in between.

Here's SeqAnswers' thread about SSPACE, and here's the SeqAnswers thread about GapFiller.

Answer 2

[Rayan Chikhi]

There's Mapsembler2 that can help you extend / visualize the neighborhood of a single contig, even if you have no other contigs.