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Old 06-06-2014, 05:23 PM   #8
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Thanks SES, that solved it. I guess all outputs must be specified. I've attached the new graphs and updated the inline images in the first post.

COPE performed much better when I set the flag "-N 0" because 5% of my synthetic reads contain an N, so I used that flag, but it was unstable and seg-faulted at and value of -c under 0.92. I included both settings, "-N 1" (default) and "-N 0". Overall it was very close to FLASH when I swept through the -c parameter (match ratio cutoff) from 1.0 to 0.75 (the default) - slightly better with -N 1 (but unstable) and slightly worse with -N 0 (but stable). There are also -d and -B parameters that probably impact the merge rate, which I left at the default, so as with most of the other programs, it's still possible that better results could be achieved. Sample command:

./cope -a /dev/shm/r1.fq -b /dev/shm/r2.fq -o /dev/shm/cmerged.fq -2 /dev/shm/r1_unconnected.fq -3 /dev/shm/r2_unconnected.fq -m 0 -s 33 -c 1.0 -u 150 -N 0 1>cope.o 2>&1

I also added fastq-join (from ea-utils), which was generally outperformed by FLASH. I swept through the -p (from 0 to 25) and -m (from 4 to 12) parameters; only the -p sweep is shown, as it gave better results. Sample command:

fastq-join r1.fq r2.fq -o fqj -p 0

These were similar in speed - both were much faster than PEAR and slightly slower than BBMerge or FLASH, when those three were limited to a single thread. fastq-join is slightly faster than COPE.
Attached Images
File Type: png BBMerge_ROC_log.png (30.1 KB, 1092 views)
File Type: png BBMerge_Speed3.png (23.2 KB, 1080 views)
File Type: png BBMerge_ROC_linear.png (27.5 KB, 1100 views)

Last edited by Brian Bushnell; 06-06-2014 at 05:26 PM.
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