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) |
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