Code 1.

Sequencing data quality control: The bash script used to run pRESTO.

FilterSeq.py trimqual -s *.fastq PairSeq.py \   --coord illumina \   -1 *R1*trimqual-pass.fastq \   -2 *R2*trimqual-pass.fastq AssemblePairs.py align \   --rc tail --coord illumina \   -1 *R1*pair-pass.fastq \   -2 *R2*pair-pass.fastq FilterSeq.py length -n 100 -s *assemble-pass.fastq FilterSeq.py maskqual -s *length-pass.fastq FilterSeq.py missing -s *maskqual-pass.fastq