--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero2/deinterleave_fastq.sh	Fri Nov 09 11:30:45 2018 -0500
@@ -0,0 +1,30 @@
+#!/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)
+# 
+# Latest code: https://gist.github.com/3521724
+# Also see my interleaving script: https://gist.github.com/4544979
+# 
+# Inspired by Torsten Seemann's blog post:
+# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html
+
+# Set up some defaults
+GZIP_OUTPUT=0
+PIGZ_COMPRESSION_THREADS=10
+
+# If the third argument is the word "compress" then we'll compress the output using pigz
+if [[ $3 == "compress" ]]; then
+  GZIP_OUTPUT=1
+fi
+
+if [[ ${GZIP_OUTPUT} == 0 ]]; then
+  paste - - - - - - - -  | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2
+else
+  paste - - - - - - - -  | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2
+fi