From our recent HiSeq runs, we are taking unmapped reads from BAMs and assembling. Can someone recommend a good workflow to get the most out of unmapped reads? Current plan is:
- Assemble using Abyss (or some paired-end assembly tool)
- Get contigs more than 200bp (randomly chosen threshold--open to ideas) and blast against hg18
- Take unmatched contigs and blast to see non-hg hits
Any ideas/suggestions welcome1
Current goal is to check for "non-human" DNA in the sample, with the hope that reads that did not align against hg18 might have a homology with something else ...