Mapping of Raw Illumina Reads

Raw reads were all treated comparably before being mapped to a specific reference genome, which varied depending on the analysis. We used Cutadapt v1.8.1 (Martin 2011) to trim Illumina adapter sequences from the ends of reads and remove reads shorter than 30 bp. We merged overlapping read pairs using FLASH v1.2.1 (Magoč and Salzberg 2011) and default parameters. We mapped the trimmed merged and unmerged reads to the respective reference sequences using BWA v0.7.15, the mem algorithm, and default parameters (Li and Durbin 2009). We further processed the mapped reads using SAMtools v1.3.1 (Li et al. 2009) to remove duplicates and reads of low mapping quality (<30).