MaSuRCA, pre-processing and post-assembly improvements

Question

[margab]

I'm using MaSuRCA to do a hybrid assembly using Nanopore (MinION) and Illumina (HiSeq X Ten) data. Do you suggest using any pre-processing tool or make any post assembly improvements (ex. polishing and gap closing)? I have read that it doesn't need any pre-processing tool.

Thanks in advance!!!

[jean.elbers]

I haven't used MaSuRCA, but it makes sense to do quality and adapter trimming of the Illumina reads before inputting them into the MaSuRCA pipeline. I am not sure sure what to advise if you should do polishing or gap closing, but it is worth a try.

Answer 1

[Corentin]

MaSuRCA specifically advise users not to preprocess the data (https://github.com/alekseyzimin/masurca):

IMPORTANT! Do not use third party tools to pre-process the Illumina data before providing it to MaSuRCA, unless you are absolutely sure you know exactly what the preprocessing tool does. Do not do any trimming, cleaning or error correction. This will likely deteriorate the assembly.

I think MaSuRCA include a read correcting step in its pipeline.

Post processing is up to you. I would advise you to try different things and check your assembly quality before/after the post-processing.