Quality Filtering
Samples were run through FastQC v 0.11.9 (Andrews 2010) and CutAdapt v 1.18 (Martin, 2011) for quality filtering and additional checks for adapter removal. Phred scores were required to be ≥ 20 averaged across each read, and the command for cutadapt was: cutadapt –report=minimal -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o {R1_output.fastq} -p {R2_output.fastq} {R1_input.fastq.gz} {R2_input.fastq.gz}.
In order to assess the overall read quality, prinseq v 0.20.4 (Schmieder & Edwards, 2011) was run on each individual library preparation to determine the proportion of low quality reads. ‘perl prinseq-lite.pl -fastq {R1.fastq} -out_format 3 -derep_min 4 -log {NAME}.fastq.log -min_qual_mean 20 -verbose’. This data was run for evaluative purposes and not passed through the CHIIMP genotyping pipeline (Barbian et al., 2018) as the only requirements for that pipeline is for the adapters to be removed via CutAdapt. All quality data is summarized in Table 3.