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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!
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!