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Old 11-24-2015, 04:49 PM   #1
thomasblomquist
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Location: Ohio

Join Date: Jul 2012
Posts: 68
Default Partial Order Alignment Step

I'm running through Jared and Nick's Nature Methods de novo assembly approach on my Lambda burn-in FAST5 data. Just to get the pipeline up and running and some familiarity using a focused data set.

I've successfully converted FAST5 to FASTA using poretools. Using the nanocorrect pipeline, I've performed the DALIGNER steps, and then now am processing using the Partial Order Alignment step using poaV2.

It is working and the corrected.fasta file is growing... slowly. I've been tailing the file and the output when blasted is giving me 95% accuracy to NCBI refseq Lambda phage sequence. It's been chuggin along for a day. I have a 16 core 3.7 Ghz setup with 64 GB of ram, and plenty of SSD drive space to spare. It's only using a single thread (based on my system process utilization). And it's only sucked up 150 MB of working RAM.

Wondering what others have done to parallelize this step, or what can be done for speed up?
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