coverage Author: Abraham Guerrero Email: [email protected] and [email protected] Version 0.1

Script to calculate the genome coverage from paired-end fastq files the script works with: Samtools (Version: 1.2) http://www.htslib.org/download BWA (bwa-0.7.12) Burrows-Wheeler Aligner http://bio-bwa.sourceforge.net

analyze the results with: BAMStats (BAMStats-1.25) http://bamstats.sourceforge.net or Qualimap (qualimap_v2.2) http://qualimap.bioinfo.cipf.es

example coverage.sh Reference.fasta File_R1.fastq File_R2.fastq Results