1. Data Quality Check (QC)

Because sequence reads are generated differently by different sequencers we will also have to use different tools to analyse the data quality for these.

Illumina QC

For Illumina (and I think PacBIO - CHECK!) we can use, e.g., FastQC:

fastqc -t XX -o fastqc file_1.fq.gz file_2.fq.gz

Oxford Nanopore QC

For ONT data we can use the R based software MinIONQC

MinIONQC.R -i sequencing_summary.txt -o MinIONQC_results/ -p 10 -f 'pdf'