--- a/SeqSero2S/bin/deinterleave_fastq.sh	Fri May 15 17:55:16 2026 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#!/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