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cat file.fa | awk '$0 ~ ">" {print c; c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' |
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#!/bin/bash | |
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] | |
# | |
# Deinterleaves a FASTQ file of paired reads into two FASTQ | |
# files specified on the command line. Optionally GZip compresses the output | |
# FASTQ files using pigz if the 3rd command line argument is the word "compress" | |
# | |
# Can deinterleave 100 million paired reads (200 million total | |
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) | |
# |
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#!/bin/sh | |
# | |
# a simple way to parse shell script arguments | |
# | |
# please edit and use to your hearts content | |
# | |
ENVIRONMENT="dev" |