Short read toolbox: Difference between revisions
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Revision as of 15:48, 23 July 2010
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 avaliable 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 - GMOD.
List of short-read quality control software
- TileQC - Requires R, RMySQL and MySQL.
- Short Read Toolbox - Scripts for quality control of Illumina data.
List of sequence format information
- Short Read Toolbox - Scripts for quality control of Illumina data.
- FASTQ - Wikipedia's FASTQ page.
- FASTA - Wikipedia's FASTA page.
List of alignment format information
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
- RGA - Perl script which calls blat to assemble short reads.
List of assembly viewers
List of alignment programs
List of 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.