How To Increase Contig Length For Gap Filling ?

Question

[HG]

Hi Everyone I have a doubt about post assembly gap filling. After assembly is it possible increase the contig length with some mapping program Such as GapFiller/Images/Price. If i used same data set as earlier i have already used for assembly. How it is possible to increase the length of contig if former and later program used same algorithm or else can any one suggest me what will be the ideal way to reduce the number or Gap in draft genome??

Thanking you in advance!

Answer 1

[Adrian Pelin]

Unless you are doing this for an organellar genome, I would advise against it. The reason contigs break, is because often there are multiple ways to extend the contig, and the assembler cannot decide which way to correctly extend it. This is often due to repetitive regions which paired end information cannot resolve. Extending contigs in these cases is not advisable. Organellar genomes usually do not have such repetitive regions.