Increase Newbler Input Read Size

[CastleR]

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!!!

[gconcepcion]

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!!!

Why are you assembling PacBio data with 454 assembler?

You should use SMRTAnalysis 2.3 instead

[CastleR]

What tools in SMRTAnalysis can do de novo assembly of 2kb fragments? HGAPv3 does a poor job compared to Newbler. Newbler actually does a great job, I just need to know how to increase the input read size threshold.

[gconcepcion]

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.

[rhall]

What is the use case for assembling CCS data? If the dataset is small, tiling a few amplicons for a viral genome, then minimus may be a viable alternative, otherwise Celera Assembler can be parameterized correctly to assembly CCS sequences.

[flxlex]

Newbler 3 will take longer reads, but I can't remember the limit, either 20kb, 30kb or 40kb. You could also try the Canu assembler, or FALCON.

[CastleR]

Thanks to everyone for the advice!!!