Does anyone know if there is a command to increase the input read size for a Newbler de novo assembly? I'm trying to use some 2-3kb PacBio CCS reads, but of course the max input read size is 1,999bp (at least in v2.6, which is what I'm using). Maybe a newer version has this option? Thanks!!!
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Originally posted by CastleR View PostDoes anyone know if there is a command to increase the input read size for a Newbler de novo assembly? I'm trying to use some 2-3kb PacBio CCS reads, but of course the max input read size is 1,999bp (at least in v2.6, which is what I'm using). Maybe a newer version has this option? Thanks!!!
You should use SMRTAnalysis 2.3 instead
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Well, if you have enough coverage, HGAPv3 should do a good job. If you have lower coverage, but higher quality CCS reads, than you might be right, Newbler may be a better option for you. Unfortunately I haven't used newbler in many years and can't guide you any further.
What kind of pre-CCS subread coverage do you have? If you have >30X (60X+ would be ideal) then you should just run HGAPv3 with your pacbio subreads.
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