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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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Short reads pre-processing before polishing #73

Open aureliendejode opened 3 years ago

aureliendejode commented 3 years ago

Question or Expected behavior I have a reference genome obtained after CANU assembly, purge_dups and long reads polishing with arrow. I'd like to polish with short reads using Next_polish. Should I use raw Illumina reads or do some pre-processing (e.g. reads trimming, remove low quality reads ...) of the short reads before using them for polishing ?

Thank you

moold commented 3 years ago

Yes

aureliendejode commented 3 years ago

Ok good. My next question is there a recommend depth of coverage for polishing ? More precisely a maximum depth of coverage because I have close to 500X of Illumina raw reads, but I guess there is no need to use all of it ?

moold commented 3 years ago

I do not test, but you can try to set -max_depth to control haw many reads are used to polish, see here