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#!/usr/bin/perl | |
# Usage: gunzip -c graph.asqg.gz | asqg2dot.pl ['<node_label_regex>'] > graph.dot | |
use strict; | |
use warnings; | |
my $bidirected = 1; | |
my $highlight_vertex_regex = shift @ARGV || ''; | |
my %vertex_labels; |
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#!/bin/bash | |
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] | |
# | |
# Deinterleaves a FASTQ file of paired reads into two FASTQ | |
# files specified on the command line. Optionally GZip compresses the output | |
# FASTQ files using pigz if the 3rd command line argument is the word "compress" | |
# | |
# Can deinterleave 100 million paired reads (200 million total | |
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) | |
# |
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#!/bin/bash | |
# Usage: quality_value_summary.sh < in.fastq > quality_stats.txt | |
# Inspired by Torsten Seemann's blog post: | |
# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html | |
# Inspired by: | |
# http://www.unix.com/shell-programming-scripting/37305-how-convert-hex-value-dec.html | |
paste - - - - | \ | |
cut -f 4 | \ | |
xxd -g 1 -c 1 -p | \ | |
grep -v '0a' | \ |
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library Illimina_pe 200 500 ^(AGRF).*$ | |
# Note sure if the following single-ended "library" is valid for AMOS: | |
library 454_se 0 0 ^(GKUZBF401|GKUZBF402|GK7W4KZ01|GK7W4KZ02|GK538RQ01|GK538RQ02|GK0HZXL01|GK0HZXL02|F196STF01|F196STF02|F4S7VAM01|F4S7VAM02|F5ZSAHT01|F5ZSAHT02|F6J8SXW01|F6J8SXW02).*$ | |
library 454_3kb 1000 5000 ^(GK33D5G01|GK33D5G02|GK9RFDF01|GK9RFDF02|GLBLI5G01|GLBLI5G02|GLDJ2JW01|GLKV9FY01).*$ | |
library 454_20kb 8000 32000 ^(F5XZBDV01|F5XZBDV02).*$ | |
pair ^(.+?)_left.*$ ^(.+?)_right.*$ | |
pair ^(.+?)/1.*$ ^(.+?)/2.*$ |
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#!/usr/bin/perl | |
# | |
# Convert contigs of an ACE file into a FASTA file. | |
# Usage: ace2fas.pl < my.ace > my.fas | |
# | |
use strict; | |
use warnings; | |
while(<>){ | |
next until /^CO\s+(\S+).+?$/; # read ACE file till next contig starts |
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#!/bin/bash | |
# | |
# NOTE: This may not entirely work! I couldn't quite get this working on my CentOS release 5.6 (Final) box | |
# | |
# References: http://www.freelists.org/post/mira_talk/header-file-missing-in-my-configlog,7 | |
# https://svn.boost.org/trac/boost/ticket/5917 | |
# http://permalink.gmane.org/gmane.comp.lib.boost.user/69898 | |
#################### | |
# Specify versions # |
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#!/usr/bin/perl | |
# | |
# Usage: sspace_evidence2agp.pl formattedcontigs.fasta < final.evidence > out.agp 2> out.stderr | |
# e.g. sspace_evidence2agp.pl intermediate_results/standard_output.formattedcontigs.fasta < standard_output.final.evidence > standard_output.agp 2> standard_output.agp.stderr | |
# | |
# What this script does: | |
# 1) Uses the *.final.evidence file created by SSPACE to generate an AGP v2.0 file. | |
# 2) Uses information in the *.formattedcontigs.fasta file to recover the original contig | |
# names. | |
# 3) Non-positive length gaps are output as component_type=U and gap length 100, as per the |
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#!/bin/bash | |
apt-get update | |
apt-get -y dist-upgrade | |
apt-get -y install ubuntu-desktop gnome-session-fallback python-software-properties | |
add-apt-repository -y ppa:freenx-team | |
apt-get update | |
apt-get -y install freenx | |
cd /tmp | |
wget https://bugs.launchpad.net/freenx-server/+bug/576359/+attachment/1378450/+files/nxsetup.tar.gz | |
tar xzf nxsetup.tar.gz |
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#!/bin/bash | |
export WORKSHOP_NAME="ACAD" | |
export PARENT_DIR="/mnt" | |
export SUDO_USER="ubuntu" | |
export TRAINEE_USER="ngstrainee" | |
export TMPDIR=/mnt/tmp | |
# set the timezone | |
TZ="Australia/Adelaide" | |
echo "$TZ" > /etc/timezone |
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#!/bin/bash | |
# Usage: fastq2fasta.sh < in.fastq > out.fasta | |
# Taken from http://stackoverflow.com/a/10359425/1413849 and happens to | |
# be able to convert 10 millions reads in 14 seconds!! | |
# The fastest converter I've seen! | |
sed -n '1~4s/^@/>/p;2~4p' |
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