Recommendation for data QC before assembly

[dplichta]

Do you recommend any QC on the short and / or long reads before submitting to OPERA-MS for the hybrid assembly of metagenomic samples?

For short reads that would include removing adapters, trimming on low quality basepairs, removing non-microbial DNA. Not sure what's the standard is for long read data.

[jsgounot]

Hello,

I don't have specific recomandation for quality trimming since (1) this depend to your dataset and (2) the impact of trimming is still not very known. Note that OPERA-MS will first produce a short-reads assembly using Megahit which will be further processed with long-reads. You can read this concerning the impact of short-reads trimming on Illumina assemblies. Concerning long-reads, impact of quality trimming is even less known since evolution of Nanopore sequencing constantly impact this aspect. However I would recommend to remove adapters and non-microbial DNA for sure. Removing low quality basepairs will depend of the quality of your input reads, you should check whether removing those does not impact too much the reads length.

Regards,
jsgounot