Post date: Sep 09, 2013 10:14:1 PM
I used xng to assemble the GBS consensus sequences from the admixture project to Alex's first draft of a L. melissa genome. I did this to evaluate how much of the genome that is represented in our GBS data is also in the genome. The relevant files, including the xng script, reference [lyc_allpaths_1sep13_1chr.fasta], and GBS consensus sequences [lycaeides_gbscontigs_reference.fasta] are in node5:/node5raid/assem/lyc_gbs_by_wg/. The results were not great. We assemble 60,363 of the 252,000 GBS sequences (24%). I am not yet sure whether I would have more luck with bwa, and I don't know whether the genome draft included all contigs and scaffolds, or a subset of longer scaffolds. We clearly have more work to do.