Sequencing tools | Assess and clean sequncing files from non-human reads with kraken2

[efigb]

Explain how to run kraken2 in the cluster to identify non-human sequences and clean it if necessary. This was set up from 2 source files:

• Directly from fastq files to use the clean ones for downstream analysis
• From bam files to check contamination in specific steps of a pipeline already ran to infer the influence of other species reads on the variant calling (for instance in deepUMI)