In Shelly’s GitHub Issue for this S.salar project, she also requested a MultiQC report for the trimming (completed on 20201029) and the genome alignments (completed on 20201103).

I ran MultiQC on Mox using a build node and no script, since the command is so simple (e.g. multiqc .) and so quick.

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RESULTS

Output folder:

• 20201106_ssalar_multiqc_fastp-hisat2/

MultiQC report (HTML)

• 20201106_ssalar_multiqc_fastp-hisat2/multiqc_report.html

A couple of notes:

1. The [fastp](https://github.com/OpenGene/fastp) trimming results are reported with sample names with a _1. This is an unfortunate mistake with name parsing. The results are comprised of both Read 1 and Read 2 FastQ data; not just Read 1.

2. The HISAT2 results also suffer from a poor filename that ends with .err. Despite the name, these files actually contain the alignment summary data.