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