genomic_DNA Seq of Colletotrichum higginsianum: strain MAFF305635
The raw read files (.fastq files) underwent quality control analysis using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the quality checked forward and reverse reads were trimmed separately with cutadapt (v1.14; https://cutadapt.readthedocs.io/) with parameters: -u 5 -u -5 -q 25 --trim-n --max-n 5 --minimum-length=80 (forward reads) and -u 5 -u -25 -q 25 --trim-n --max-n 5 --minimum-length=80 (reverse reads). The resulting reads were subsequently processed so that only read pairs were both the forward and reversed read fulfilled the criteria were kept for further analyses. Reads were aligned as single reads using Bowtie2 (v2.2.9) with default parameters to the reference assembly of strain IMI 349063 (accession: GCA_001672515.1)