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Old 02-29-2016, 04:18 AM   #1
Marcela Uliano
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Location: Berlin, Germany

Join Date: Apr 2012
Posts: 18
Default SSPACE run time - how to improve performance

Hey guys,

I'm denovo assembling a 1Gb mussel genome. And I've
been using PacBio CCS reads and SSPACElong.pl to scaffold my Illumina
assembly with SOAP. It's looking great, but its taking a long time!

SOAP has created millions of scaffolds, and I have 13x coverage of PacBio. SSPACE is using 30Gb of RAM in the last 4 days now, and has created around 200 scaffolds... I have given the parameter -t 12 to the program, and I guess its used during the blasr step..

I was wondering if there is anything else I could do to improve the time performance of the software?

My command line: >perl SSPACE-LongRead.pl -t 12 -c genome.fasta -p ccs.reads -b output.folder

Thank you so much!
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