Post date: Nov 08, 2013 11:44:13 PM
The alignments finished successfully. About 40% of the sequences aligned to the melissa reference genome. This is alright, but not amazing (e.g., we get better results with timema). A summary of the number of reads, number aligned and proportion aligned is in numaligned.txt on the melissaGbs2genome directory (with the alignments). I will think about this more, but for now I am moving forward towards variant calling.
I am now using samtools to compress, sort and index the alignments via a perl wrapper for batch submission to the dorc clusters.