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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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PB human genome coverage upper limit? #105

Closed isantana-bio closed 5 years ago

isantana-bio commented 5 years ago

Is there a recommended upper limit for pacbio data, the examples you shared use up to 93x of high error reads and up to 28x of CCS. Should the presets below and any other defaults remain the same if the coverage is twice as much?

sequel (high error reads):preset3: -p 19 -AS 2 -s 0.05 -L 5000 sequel ccs: preset4: -p 21 -k 0 -AS 4 -K 0.05 -s 0.5

Thanks!

ruanjue commented 5 years ago

wtdbg2 has two options -g <gsize> and -X 50.0, it will select 50X longest reads. If you want to use more in assembly please change -X. About the presets, you can increase -p 19 to -p 21 if have much more data.

isantana-bio commented 5 years ago

Will test with those params. Thank you.