So, working on a de novo assembly using Canu, and it seems to be VERY sensitive to the genomeSize=XXX parameter which is required. As it is a new project, no one has an actual "size" on it (checked T Ryan Gregory's site...nothing similar there either).
So, I am using BBMap suite, specifically...the "kmercountexact.sh" component. Waiting on a compute node right now with >64GB of ram to run, but have it set as follows: kmercountexact.sh in=filtered_subreads.fastq khist=khist.txt peaks=peaks.txt out=genomesize.txt
As Brian Bushnell is active on here, I was hoping to inquire about using this on PacBio specifically...anything I need to be more specific about on the options? Also, can I specify both of my PacBio files as arguments? I have both a .fastq of the long reads as well as a .fasta of much shorter reads supplied by the sequencer people. I know it can do PE files as in= and in2=, but what about to essentially "single" reads?
So, I am using BBMap suite, specifically...the "kmercountexact.sh" component. Waiting on a compute node right now with >64GB of ram to run, but have it set as follows: kmercountexact.sh in=filtered_subreads.fastq khist=khist.txt peaks=peaks.txt out=genomesize.txt
As Brian Bushnell is active on here, I was hoping to inquire about using this on PacBio specifically...anything I need to be more specific about on the options? Also, can I specify both of my PacBio files as arguments? I have both a .fastq of the long reads as well as a .fasta of much shorter reads supplied by the sequencer people. I know it can do PE files as in= and in2=, but what about to essentially "single" reads?
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