Post date: Sep 12, 2013 8:17:35 PM
I added the linkage group information (number and order) to the genome fasta file (see addlginfo.pl). The new draft genome is called lg_timemaGeonme.fasta and it is in data/timema/draft_genome/draft0.2/. I then indexed the genome with bwa with the following command:
bwa index -a bwtsw lg_timemaGenome.fasta
This is the version of the genome that I will assemble the whole genome resequence data to. Also note, I am using bwa version 0.7.5a-r405.