4.5 years ago by
France, Lille, CNRS
In my opinion, two really competitive stand-alone gap closers are:
Your question needs to be reframed though (it appears that you want to do scaffolding). Gaps, in the assembly context, refer to sequences of undetermined nucleotides (NNN...NNN) inside scaffolds.
If you only have contigs (which do not have gaps by the previous definition) and paired-end reads, what you want is to perform scaffolding (another type of software does that). Gap-closing is a later step which consists in replacing these undetermined regions by the actual sequence.
For scaffolding, there are many options, I would recommend SSPACE or a recent one that I haven't tested, SCARPA.