Quality check in long read (ONT, PacBio) bam files

Question

[shinyjj]

Hi long read people,

When you run minimap2 with fastq files, are there any quality check you do before feeding to LR algorithms? I know if the data quality is good, there is no need, but I want to see how other people do it. I heard looking at MAPQ or coverage is good idea, but want to hear some specific pipelines. For example, in short read, after aligning with STAR, sometimes trimming/cleaning data is recommend using bbduk.

Answer 1

[GenoMax]

This is before alignment. pycoQC (LINK) is one option but it does require a sequencing_summary* file that can only be found in the original run folder.

WouterDeCoster has some program available here: https://github.com/wdecoster/nanopack