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emyounglab / prymetime

Pipeline for Recombinant Yeast genoMEs That Identifies Markers of Engineering
MIT License
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Format of genome_size input? #36

Closed evautumn closed 2 years ago

evautumn commented 2 years ago

Hello, What is the format of the genome_size input? Is it in bp, Mbp, or Gbp? How does this feature affect the program? If the program predicts a genome size of 11 Mb with the nanopore and illumina files, and my genome-size input is 14 Mb, does it change anything? If I write -genome-size 10845397 (as in 10845397 bp), is this acceptable? Thanks!

sjtrauber commented 2 years ago

Yes, that is acceptable. Adding genome size to Prymetime is for Flye to run more effectively, but it is completely optional for Flye with the 2.8 update. For Prymetime, without genome-size specified, it defaults to set genome-size to 12100000bp.