###Contact Glennis Logsdon at glogsdon@uw.edu if you have any questions###

Raw fastqs were processed with Sickle, FastQC, and TrimGalore (commands below) and aligned to the T2Tv1 genome or HG002 genome with BWA-MEM (commands below). BAMs were filtered with samtools -F 2308 or samtools -q 10 -F 3852.


Sickle (v1.33) command:
sickle pe -t sanger -q 20 -l 100 -f {R1.fastq.gz} -r {R2.fastq.gz} -o {trimmed_R1.fq} -p {trimmed_R2.fq} -s {singles.fq}

FastQC (v0.11.7) command:
fastqc {trimmed_R1.fq} {trimmed_R2.fq} {singles.fq}

TrimGalore (v0.6.6) command:
trim_galore --paired --retain_unpaired --length 100 --illumina --stringency 5 --fastqc {trimmed_R1.fq} {trimmed_R2.fq}

BWA-MEM (v0.7.17) command:
bwa mem -t {threads} -k 50 -c 1000000 {ref_index} {trimmed_R1.fq} {trimmed_R2.fq} | samtools view -bS -F 2308 | samtools sort -m 8G -T {tmp} -o {out.bam}