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!
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!
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