PacBioToCA

In running pacBioToCA, we found that the amount of PBcR was influenced by the parameter of genomeSize.

Short reads: 100X, long reads: 200X, w/wo genome size

pacBioToCA -l viaMiseq -s pacbio.spec  -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 miseq.100X.frg.bz2

pacBioToCA -l viaMiseq -s pacbio.spec  -t 10 -partitions 200 fastqFile=filtered_subreads.200X.fastq.bz2 genomeSize=4650000 miseq.100X.frg.bz2

Short reads: 118X, long reads: one ~ four SMRT cell reads, w/wo genome size