I am working on a genome assembly and now I am working on gap closing.
There's one approach I have been using for some time and it has been proved to be more efficient and accurate than gap closing software: 1) mapping and extracted the initial consensus with gaps filled by Ns. 2) visualizing the mapping track, check the reads flanking the gaps, especially the mismatched ends against the reference. 3) manually extend the contigs using read end information. 4) redo these three steps to extend contigs 5) after extend the contigs for over one or two hundreds bps, blast the contig ends to each others and see if two contigs connect.
But this method relies on the mapping software has setting of minimum read length, I used CLC workbench before for gap closure but now I worked in other lab and we cannot afford CLC.
Have you guys known any softwares can set the minimum read length?