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Old 03-04-2012, 08:38 AM   #3
nilshomer
Nils Homer
 
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Location: Boston, MA, USA

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Copied here from http://sourceforge.net/mailarchive/m...sg_id=28915492

I am working on benchmarking the samtools commands today, and will post back.

Quote:
A 4GB SAM file was used on a dual-hex-core (12 cores) computer. I
benchmarked compression then decompression, making sure the resulting files
were the same. Decompression seems to be limited by IO.

Name Compression Time Decompression Time
bgzip 485.64 39.93
pbgzip -n 1 481.57 40.02
pbgzip -n 2 240.85 41.03
pbgzip -n 4 122.05 41.79
pbgzip -n 8 63.17 41.17
pbgzip -n 12 43.12 41.65
pbgzip -n 16 39.59 41.48
pbgzip -n 20 37.03 42.41
pbgzip -n 24 34.90 47.24
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