An tutorial for running deepconsensus about deepconsensus

[MariaNattestad]

Hi thanks for sharing this! Was there anything you felt was missing from the quick start? We recently updated this to include detailed parallelization instructions, showing how to run ccs with --chunk, so please take a look!

[shengxinzhuan]

@MariaNattestad Hi, MariaNattestad! Thanks to reply! I know how to run ccs with --chunk. But in China, we always got the ccs.bam from the sequencing company. So I don't need to filter the ccs.bam again, and move --chunk in actc. By the way, the ccs with --chunk and without --chunk are spend the same time on my test. If we need to filter the ccs.bam by ourself, --chunk may be more recommanded cause it can run again from the breakpoint.

[MariaNattestad]

Thanks for this context. I want to make sure to mention that in the quick start we do recommend running ccs yourself with --all so that DeepConsensus has the chance to rescue some reads that would have gotten filtered out as being below (usually) Q20 when ccs was run with default settings. Your yield above Q20 will often increase significantly if you are able to rerun ccs with --all.

[shengxinzhuan]

@MariaNattestad Thanks to reply! I will try again if the reads depth do not satisficated to assembly an genome.

[MariaNattestad]

@shengxinzhuan sounds good! I'll close this issue, but feel free to open a new one (so we get notified) if you have any new issues or questions. We want to understand the problems that our users face using DeepConsensus in practice!

[shengxinzhuan]

@MariaNattestad ok， I will open a new one if i meet new problem. Thanks!