Iterative Mapping And Assembly For Gap Elimination (Images)

Question

[HG]

Hi everyone i finished listeria genome assembly with Spades, after that i used ABACAS for scaffolding and ordering of the contig but i have few gap after scaffolding. Now i want to fill gap in insilico method do anyone suggest which will be best methods to fill the gap?? i already tried with IMAGES, but i did not get any suitable manual for this also. Please help me out Thanks all.

Answer 1

[cts]

You could try out GapFiller or GapCloser which is part of SOAPdenovo

[HG]

Is GapFiller a free software ???

[cts]

It's "free as in beer". You do annoyingly have to give them your email address and name.

[HG]

could you please suggest me how to use it i already tried according to manual but failed ......please help me out