Evaluation of short read aligners with base qualities

[NicolaP]

Hi!

I am trying to evaluate the performances of the short reads aligner we developed in my research group (bw-erne), and I came across this useful website: http://www.bioplanet.com/gcat , which permits to perform tests (download fastq -> align -> upload bam), automatically computing the precision of the tool used and comparing the results with popular aligners.

However, GCAT does not simulate base qualities. Since our aligner implements a quality-based heuristic (like bowtie), we would be interested in something similar, but with also (realistically) simulated qualities. Does anybody know if there is something like that on the web?

thank you!
N

[GenoMax]

Perhaps ART: http://www.niehs.nih.gov/research/re...tatistics/art/

[NicolaP]

Perhaps ART: http://www.niehs.nih.gov/research/re...tatistics/art/

Thank you! I'll try it.

[scami]

Thanks!

Hi!

I am trying to evaluate the performances of the short reads aligner we developed in my research group (bw-erne), and I came across this useful website: http://www.bioplanet.com/gcat , which permits to perform tests (download fastq -> align -> upload bam), automatically computing the precision of the tool used and comparing the results with popular aligners.

However, GCAT does not simulate base qualities. Since our aligner implements a quality-based heuristic (like bowtie), we would be interested in something similar, but with also (realistically) simulated qualities. Does anybody know if there is something like that on the web?

thank you!
N

Thanks for sharing this link! It sounds interesting! I will try it on my pipeline!