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| =Short read toolbox=
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| This page has been created to help list resources for working with high throughput sequencing data. | | This page was created to help list resources for working with high throughput sequencing data. You can also check out our individual lab pages to see updates on methods -- [[Cronn Lab]] or [[Liston:Lab]] -- to see updates on methods . |
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| =Short Read Workshop= | | =Disambiguation= |
| Download Presentations and Training Modules from our Recent Short Read Workshop, "An introduction to next-generation sequencing". Presented at the Botany 2010 Meeting in Providence, R.I.
| | Short read toolbox may refer to: |
| | | * [http://brianknaus.com Short read toolbox] - The website of Brian J. Knaus. |
| * [[media:Botany2010_workshop_agenda.pdf| Meeting Agenda]]
| | *[[Short read toolbox Botany2010]] - Resources provided at the Botany 2010 conference. |
| * [[media:Botany2010_workshop_summaries.pdf| Presentation Summaries and Suggested Reading]]
| | *[[Short read toolbox Botany2012]] - Resources provided at the Botany 2012 conference. |
| * [[media:Botany2010_workshop_training.pdf| Example Module A: Assembling chloroplast genomes from short reads]]
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| * [[media:Botany2010_workshop_training.pdf| Example Module B: Programs and data to download]]
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| =Platforms=
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| Currently available platforms:
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| *[http://www.illumina.com/ Illumina] - Illumina (formerly Solexa).
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| *[http://www.454.com/ 454] - 454/Roche.
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| *[http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html SOLiD] - ABI by Life Technologies.
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| Anticipated technologies:
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| *[http://www.iontorrent.com/ Ion Torrent Semiconductor] - Ion Torrent.
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| *[http://www.pacificbiosciences.com/ SMRT] - Pacific BioSciences.
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| *[http://www.nanoporetech.com/ Nanopore] - Oxford Nanopore Technologies.
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| =Online short-read resources=
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| *[http://seqanswers.com/ SEQanswers] - Online forum for next generation sequencing.
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| *[http://seqanswers.com/forums/showthread.php?t=43 SEQanswers software post] - Post of software available for next generation sequence data.
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| *[http://seqanswers.com/wiki/Category:Bioinformatics_application SEQwiki] - SEQ Answers wikilist of bioinformatic applications.
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| *[http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/ De novo tips] - Blog on de novo assembly.
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| *[http://genome.ucsc.edu/index.html UCSC Bioinformatics] - UC Santa Cruz's bioinformatics server.
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| *[http://www.phylo.org/ Cipres] - Cipres.
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| *[http://gmod.org/wiki/Main_Page GMOD] - Generic model organism database (GMOD) project collection of tools.
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| *[http://www.biopieces.org] - Collection of bioinformatic tools
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| *[ftp://ftp.illumina.com/ Illumina Manuals] username: guest password: illumina
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| =Sequence format information=
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| *[http://brianknaus.com/software/srtoolbox/shortread.html Short Read Toolbox] - Descriptions and examples of qseq, scarf, fastq and fasta formats. Includes scripts to translate these formats to the fastq format standard. | |
| *[http://en.wikipedia.org/wiki/FASTQ_format FASTQ] - Wikipedia's FASTQ page. | |
| *[http://en.wikipedia.org/wiki/FASTA_format FASTA] - Wikipedia's FASTA page.
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| =Alignment format information=
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| *[http://samtools.sourceforge.net/ SAMtools] - SAMtools.
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| *[http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] - AMOS.
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| *[http://genome.ucsc.edu/FAQ/FAQformat.html UCSC] - UCSC's faq on file formats.
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| =Short-read quality control software=
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| *[http://www.science.oregonstate.edu/~dolanp/tileqc/index.html TileQC] - Requires R, RMySQL and MySQL.
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| *[http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC] - A quality control tool for high throughput sequence data. A Java application.
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| *[http://brianknaus.com/software/srtoolbox/shortread.html Short Read Toolbox] - Scripts for quality control of Illumina data.
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| =Open source de novo assemblers=
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| *[http://www.ebi.ac.uk/~zerbino/velvet/ Velvet] - Implements De Bruijn Graphs in C. Requires 64 bit Linux OS. | |
| *[http://www.genomic.ch/edena.php Edena] - 32 and 64 bit Linux.
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| *[http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS] - Multi-threaded de novo assembly.
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| *[http://sourceforge.net/apps/mediawiki/denovoassembler/index.php?title=Main_Page Ray] - Multi-threaded de novo assembly.
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| *[http://qsra.cgrb.oregonstate.edu/ QSRA] - Utilizes quality scores.
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| =Open source reference guided assemblers=
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| *[http://soap.genomics.org.cn/index.html SOAP] - Short Oligonucleotide Analysis Package.
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| *[http://maq.sourceforge.net/ MAQ] - Mapping and Assembly with Qualities.
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| *[http://bowtie-bio.sourceforge.net/index.shtml Bowtie] - Bowtie. An ultrafast, memory-efficient short read aligner.
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| *[http://bio-bwa.sourceforge.net/ BWA] - Burrows-Wheeler aligner.
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| *[http://rga.cgrb.oregonstate.edu/ RGA] - Perl script which calls blat to assemble short reads.
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| =Hybrid assemblers (reference guided & de novo)=
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| *[http://www.bx.psu.edu/miller_lab/ YASRA] - Yet Another Short Read Aligner.
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| *[http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-4698/index.html Aakrosh Ratan dissertation] - Description of YASRA.
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| *[[Liston:Computer_Scripts]] - Scripts for post-processing of YASRA contigs.
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| =RNA-Seq / Transcriptome=
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| *[http://tophat.cbcb.umd.edu/ TopHat] - A fast splice junction mapper for RNA-Seq reads.
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| *[http://cufflinks.cbcb.umd.edu/ Cufflinks] - Assembles transcripts, estimates their abundances, and tests for differential expression and regulation.
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| *[http://supersplat.cgrb.oregonstate.edu/ SuperSplat] - Splice junction discovery.
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| =Assembly viewers=
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| *[http://bioinf.scri.ac.uk/tablet/ Tablet] - Tablet, visualizes ACE, AFG, MAQ, SOAP, SAM and BAM formats.
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| *[http://samtools.sourceforge.net/ SAMtools] - SAMtools.
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| =Alignment programs=
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| *[http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ MAFFT] - MAFFT.
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| *[http://www.ebi.ac.uk/Tools/t-coffee/index.html T-Coffee] - T-Coffee.
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| *[http://www.ebi.ac.uk/Tools/muscle/index.html Muscle] - Muscle.
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| *[http://www.bx.psu.edu/miller_lab/ LASTZ] - LASTZ, hosted at the Miller lab.
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| *[http://mummer.sourceforge.net/ MUMmer] - MUMmer.
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| *[http://mulan.dcode.org/ Mulan] Multiple Sequence Alignment and Visualization Tool.
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| *[http://genome.lbl.gov/vista/ VISTA] Tools for Comparative Genomics.
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| *[http://asap.ahabs.wisc.edu/software/mauve/ mauve] - Multiple (bacterial) genome aligment.
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| =Sequence query programs=
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| *[http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST] - BLAST.
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| *[http://bioinfo.noble.org/plan/ PLAN] - A web application for conducting, organizing, and mining large-scale BLAST searches (limited to 1,000 queries).
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| *[http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign BLAT] - BLAT.
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| =Linux=
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| *[[media:Essential_Linux.pdf | Essential Linux]]
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| =Perl=
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| A very brief example to demonstrate file input/output.
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| Code:<br>
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| <pre>
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| #!/usr/bin/perl
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| use strict;
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| use warnings;
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| my (@temp, $in, $out);
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| my $inf = "data.fq";
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| my $outf = "data_out.fq";
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| open($in, "<", $inf) or die "Can't open $inf: $!";
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| open($out, ">", $outf) or die "Can't open $outf: $!";
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| while(<$in>){
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| chomp($temp[0]=$_); # First line is an identifier.
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| chomp($temp[1]=<$in>); # Second line is sequence.
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| chomp($temp[2]=<$in>); # Third line is an identifier.
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| chomp($temp[3]=<$in>); # Fourth line is quality.
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| print $out join("\t", @temp)."\n";
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| }
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| close $in or die "$in: $!";
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| close $out or die "$out: $!";
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| </pre>
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| *[http://perldoc.perl.org/perlintro.html perlintro] - Introduction to perl with links to other documentation.
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| *[http://www.bioperl.org/wiki/HOWTO:Beginners BioPerl beginners] - Introduction to BioPerl (be prepared for object oriented code).
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| =Python=
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| *[http://docs.python.org/tutorial/ Python tutorial]
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| *[http://biopython.org/wiki/Biopython Biopython]
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| =R project=
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| *[http://www.r-project.org/ R project] - Statistical programming environment.
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| *[http://www.bioconductor.org/ Bioconductor] - R for biologists (micro-array and next generation data).
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| *[http://ape.mpl.ird.fr/ APE] - Analysis of phylogenetics and evolution R package.
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| *[http://manuals.bioinformatics.ucr.edu/home/ht-seq/ HT Sequence Analysis with R and Bioconductor]
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| =Useful links=
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| *[[User:Brian J. Knaus]]
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| *[[Cronn Lab]]
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| *[[Liston:Lab | Liston Lab]]
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