First, I am wondering if it is overkill, if I map all the illumina reads on just one contig, then do the Pilon error correction. For example, we use the entire Illumina reads to correct one contig a time?
Second, if we are correcting Pacbio contigs, do we need to use "bwa mem pacbio" command to do the alignment? Or just regular "bwa mem" command? My understanding is to use the later one, is it right?
Hi Pilon developers,
First, I am wondering if it is overkill, if I map all the illumina reads on just one contig, then do the Pilon error correction. For example, we use the entire Illumina reads to correct one contig a time?
Second, if we are correcting Pacbio contigs, do we need to use "bwa mem pacbio" command to do the alignment? Or just regular "bwa mem" command? My understanding is to use the later one, is it right?
Thanks.
George