Stampy alignment

[bair]

Hello all,

Does anybody have the experience of using stampy for alignment?

Based on stampy's document:

Fast: about 20 Gbase per hour in hybrid mode (using BWA)
Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome

Our pair of fastq file (pair end) of the same lane has less than 100m reads, 10Gbase (101bp per reads), so the alignment should be completed in one hour, but actually it took >120hrs to finish.

We use stampy 1.0.10 combined with bwa 0.5.8c, the memory using is about 7G, I just wonder that stampy needs big memory to reach its best performance.

Thanks!

[gertonlunter]

Hi,

You quote correctly from the README, but the numbers are unfortunately incorrect. Instead of 20 Gbase/hour, it is 15 hours / Gbase (as given in the paper). Apologies for the mistake.

In version 1.11 (to be released later today) I've implemented a speedup for longer reads, which should give a decent performance boost for your data set.

Best wishes
Gerton