generic, slightly insane paired end quality trimming script
#!/bin/bash | |
# trim.sh - generic, slightly insane paired end quality trimming script | |
# Vince Buffalo <vsbuffaloAAAAAA@gmail.com> (sans poly-A) | |
set -e | |
set -u | |
## pre-config | |
ADAPTERS=illumina_adapters.fa | |
SAMPLE_NAME=some_sample_name | |
IN1=in1.fastq | |
IN2=in2.fastq | |
## presets | |
PRIOR=0.4 | |
QUAL_THRESH=20 | |
time (sickle pe -t sanger -q $QUAL_THRESH \ | |
-f <(seqqs -e -p raw_${SAMPLE_NAME}_R1 $IN1 | scythe -a $ADAPTERS -p $PRIOR - 2> ${SAMPLE_NAME}_R1_scythe.stderr) \ | |
-r <(seqqs -e -p raw_${SAMPLE_NAME}_R2 $IN2 | scythe -a $ADAPTERS -p $PRIOR - 2> ${SAMPLE_NAME}_R2_scythe.stderr) \ | |
-o >(seqqs -e -p trimmed_${SAMPLE_NAME}_R1 - | gzip > ${SAMPLE_NAME}_R1_trimmed.fq.gz) \ | |
-p >(seqqs -e -p trimmed_${SAMPLE_NAME}_R2 - | gzip > ${SAMPLE_NAME}_R2_trimmed.fq.gz) \ | |
-s >(seqqs -e -p trimmed_${SAMPLE_NAME}_singles - | gzip > ${SAMPLE_NAME}_singles_trimmed.fq.gz) 2> ${SAMPLE_NAME}_sickle.stderr) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment