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Old 02-03-2017, 08:03 AM   #58
Location: East Coast

Join Date: Jul 2016
Posts: 38

Hi Brian,

I was wondering if there was a way to save the reads that are used during contig assembly, so that they can be mapped back to the generated consensus in a downstream step. I noticed the 'outd=<file>' flag will list discarded reads - anything similar for used reads?

I'm quite happy with Tadpole's ability to assemble PCR-amplified viral genomes post-illumina sequencing. I've compared it to Spades and CLC. The one thing I'd like to see what reads are getting used, discarded, etc.

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