Genome Polishing nextPolish

Question

[Umer]

HI reader,

I have generated De-novo genome assemblies for fungal Nanopore FastQ files using NextDenovo v2.5.2

For the same sample i also have Illumina 150bp PE fastQ files too.

I wanted to perform Polishing of genome assemblies using nextPolish but have some queries.

1. Should I use nextPolish or the newer nextPolish2
2. Should i use the task = best uption while providing both Nanopore and Illumina data togather ?
3. Do I need to run multiple rounds of polishing like Racon and Pilon ?

Thank you.

Answer 1

[shelkmike]

As indicated in the readme of NextPolish2, it is intended for HiFi reads (https://github.com/Nextomics/NextPolish2). Thus, it's not for Nanopore reads.
In the manual of NextPolish you may see "Please set task=best to get the best result" (https://nextpolish.readthedocs.io/en/latest/FAQ.html).
NextPolish performs several rounds (in the manual they are called "iterations" instead of "rounds", but these are synonyms) of polishing by itself, so you don't have to run NextPolish several times.

[Umer]

Thank you for clarifying. I ran only once using task=best