NextPolish for metagenome?

[123chenshixin]

Thank you for developing such an excellent tool. Since NextPolish was not tested in metagenomic data which has strain-level polymorphism(similar to haplotypes), I wondered if there were any problems with using nextpolish for metagenomic polish. If you can provide answers or share related articles, I would be very grateful!

[moold]

The accuracy of NextPolish depends on the accuracy of read alignment, and read alignment may not be able to distinguish different species genomes when mapping to metagenomes, similar to the inaccurate alignment of repeat regions. Therefore, based on this incorrect alignment, the polishing results may be inaccurate.
But, you can have a try first.