Short read toolbox

Short read toolbox

This page has been created to help list resources for working with next generation sequence data.

Online short-read resources

• SEQanswers - Online forum for next generation sequencing.
• SEQanswers software post - Post of software available for next generation sequence data.
• SEQwiki - SEQ Answers wikilist of bioinformatic applications.
• De novo tips - Blog on de novo assembly.
• UCSC Bioinformatics - UC Santa Cruz's bioinformatics server.
• Cipres - Cipres.
• GMOD - Generic model organism database (GMOD) project collection of tools.
• Illumina Manuals username: guest password: illumina

List of sequence format information

• Short Read Toolbox - Descriptions and examples of qseq, scarf, fastq and fasta formats. Includes scripts to translate these formats to the fastq format standard.
• FASTQ - Wikipedia's FASTQ page.
• FASTA - Wikipedia's FASTA page.

List of alignment format information

• SAMtools - SAMtools.
• AMOS - AMOS.
• UCSC - UCSC's faq on file formats.

List of short-read quality control software

• TileQC - Requires R, RMySQL and MySQL.
• FastQC - A quality control tool for high throughput sequence data. A Java application.
• Short Read Toolbox - Scripts for quality control of Illumina data.

List of open source de novo assemblers

• Velvet - Implements De Bruijn Graphs in C. Requires 64 bit Linux OS.
• Edena - 32 and 64 bit Linux.
• ABySS - Multi-threaded de novo assembly.
• Ray - Multi-threaded de novo assembly.

• QSRA - Utilizes quality scores.

List of open source reference guided assemblers

• SOAP - Short Oligonucleotide Analysis Package.
• MAQ - Mapping and Assembly with Qualities.
• Bowtie - Bowtie. An ultrafast, memory-efficient short read aligner.
• BWA - Burrows-Wheeler aligner.
• RGA - Perl script which calls blat to assemble short reads.

Hybrid assemblers (reference guided & de novo)

• YASRA - Yet Another Short Read Aligner.
• Aakrosh Ratan dissertation - Description of YASRA.
• Liston:Computer_Scripts - scripts for post-processing of YASRA contigs.

List of assembly viewers

• Tablet - Tablet, visualizes ACE, AFG, MAQ, SOAP, SAM and BAM formats.
• SAMtools - SAMtools.

List of alignment programs

• MAFFT - MAFFT.
• T-Coffee - T-Coffee.
• Muscle - Muscle.
• LASTZ - LASTZ, hosted at the Miller lab.
• MUMmer - MUMmer.
• Mulan Multiple Sequence Alignment and Visualization Tool.
• VISTA Tools for Comparative Genomics.
• mauve - Multiple (bacterial) genome aligment.

List of nucleotide sequence query programs

• BLAST - BLAST.
• BLAT - BLAT.

Perl

A very brief example to demonstrate file input/output.

Code:

#!/usr/bin/perl
use strict;
use warnings;
my (@temp, $in, $out);
my $inf = "data.fq";
my $outf = "data_out.fq";
open($in, "<", $inf) or die "Can't open $inf: $!";
open($out, ">", $outf) or die "Can't open $outf: $!";
while(<$in>){
  chomp($temp[0]=$_); # First line is an identifier.
  chomp($temp[1]=<$in>); # Second line is sequence.
  chomp($temp[2]=<$in>); # Third line is an identifier.
  chomp($temp[3]=<$in>); # Fourth line is quality.
  print $out join("\t", @temp)."\n";
}
close $in or die "$in: $!";
close $out or die "$out: $!";

• perlintro - Introduction to perl with links to other documentation.
• BioPerl beginners - Introduction to BioPerl (be prepared for object oriented code).

Python

• Python tutorial
• Biopython

R project

• R project - Statistical programming environment.
• Bioconductor - R for biologists (micro-array and next generation data).
• APE - Analysis of phylogenetics and evolution R package.
• HT Sequence Analysis with R and Bioconductor

Useful links

• User:Brian J. Knaus
• Cronn Lab
• Liston Lab