Short read toolbox
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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
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
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
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
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
