Hello guys, I have a really crappy denovo assembly and would like to know what is the best way to extend my contigs.
Currently I am progressing very slowly by using geneious to assemble to reference my illumina data on top of my existing contigs.
I know there is a consed script called addSolexaReads.perl that will create an ace file that has a reference sequence and reads aligned to it, the problem is, is that it does not generate a new consensus based on the reads that have been mapped to it.
What I am interested are the edges of the contigs and how could the solexa data that I have extend these edges further until 2 ends hit each other and create 1 contig by closing a gap.
I would like to make this an itterative process somehow.
Thank you.
Currently I am progressing very slowly by using geneious to assemble to reference my illumina data on top of my existing contigs.
I know there is a consed script called addSolexaReads.perl that will create an ace file that has a reference sequence and reads aligned to it, the problem is, is that it does not generate a new consensus based on the reads that have been mapped to it.
What I am interested are the edges of the contigs and how could the solexa data that I have extend these edges further until 2 ends hit each other and create 1 contig by closing a gap.
I would like to make this an itterative process somehow.
Thank you.
Comment