-output_dir : analysis output folder. -path_to_fastq : path to paired fastq.

Launch the pipeline: ./snakemake.sh > snakemake.out &

Removing adapters using cutadapt. Version 1.12. See more here : => https://cutadapt.readthedocs.io/en/stable/guide.html <=

Filtrate and remove human read using bwa. Version 0.7.15-r1140. See more here : => http://bio-bwa.sourceforge.net/ <=

Alignment on reference using bwa. Processing BAM output using samtools and generating a preconcensus. Version 1.3.1. See more here: => http://www.htslib.org/ <=

Repeat step 4 using the previous preconsensus sequence.

Compute coverage using Bedtools. Version v2.26.0. See more here: => https://bedtools.readthedocs.io/en/latest/ <=