archive:bioinformatic_tools
Differences
This shows you the differences between two versions of the page.
| Next revision | Previous revision | ||
|
archive:bioinformatic_tools [2015/07/15 20:31] ceisenhart created |
archive:bioinformatic_tools [2015/09/04 14:24] (current) 68.180.228.52 ↷ Links adapted because of a move operation |
||
|---|---|---|---|
| Line 4: | Line 4: | ||
| === Pre-Processing tools === | === Pre-Processing tools === | ||
| Tools used on reads before assembly to improve assembly quality | Tools used on reads before assembly to improve assembly quality | ||
| - | * [[bioinformatic_tools:seqprep|SeqPrep]]((https://github.com/jstjohn/SeqPrep)) Trim adapters/primers from ends of illumina reads, and merges paired illumina reads into singles if there is a user defined minimum overlap. | + | * [[archive:bioinformatic_tools:seqprep|SeqPrep]]((https://github.com/jstjohn/SeqPrep)) Trim adapters/primers from ends of illumina reads, and merges paired illumina reads into singles if there is a user defined minimum overlap. |
| - | * [[bioinformatic_tools:jellyfish|JELLYFISH]]((http://www.cbcb.umd.edu/software/jellyfish/)) Do K-mer counting on reads | + | * [[archive:bioinformatic_tools:jellyfish|JELLYFISH]]((http://www.cbcb.umd.edu/software/jellyfish/)) Do K-mer counting on reads |
| - | * [[bioinformatic_tools:quake|Quake]]((http://www.cbcb.umd.edu/software/quake/)) Do K-mer correction on reads (Can use JELLYFISH results as input) | + | * [[archive:bioinformatic_tools:quake|Quake]]((http://www.cbcb.umd.edu/software/quake/)) Do K-mer correction on reads (Can use JELLYFISH results as input) |
| Line 19: | Line 19: | ||
| == Probably Open Source Tools == | == Probably Open Source Tools == | ||
| - | * [[bioinformatic_tools:phrap|Phrap]]((http://www.phrap.org/phredphrap/phrap.html)) | + | * [[archive:bioinformatic_tools:phrap|Phrap]]((http://www.phrap.org/phredphrap/phrap.html)) |
| - | * [[bioinformatic_tools:velvet|Velvet]]((http://www.ebi.ac.uk/~zerbino/velvet/)) | + | * [[archive:bioinformatic_tools:velvet|Velvet]]((http://www.ebi.ac.uk/~zerbino/velvet/)) |
| - | * [[bioinformatic_tools:abyss|ABySS]]((http://www.bcgsc.ca/platform/bioinfo/software/abyss)) | + | * [[archive:bioinformatic_tools:abyss|ABySS]]((http://www.bcgsc.ca/platform/bioinfo/software/abyss)) |
| - | * [[bioinformatic_tools:allpaths|ALLPATHS]]((ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/)) | + | * [[archive:bioinformatic_tools:allpaths|ALLPATHS]]((ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/)) |
| - | * [[bioinformatic_tools:amos|AMOS]]((http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS_Getting_Started)) | + | * [[archive:bioinformatic_tools:amos|AMOS]]((http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS_Getting_Started)) |
| - | * [[bioinformatic_tools:arachne|Arachne]]((http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page)) | + | * [[archive:bioinformatic_tools:arachne|Arachne]]((http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page)) |
| - | * [[bioinformatic_tools:cap3_pcap|CAP3/PCAP]]((http://seq.cs.iastate.edu/)) | + | * [[archive:bioinformatic_tools:cap3_pcap|CAP3/PCAP]]((http://seq.cs.iastate.edu/)) |
| - | * [[bioinformatic_tools:celera|Celera]]((http://www.cbcb.umd.edu/research/CeleraAssembler.shtml)) | + | * [[archive:bioinformatic_tools:celera|Celera]]((http://www.cbcb.umd.edu/research/CeleraAssembler.shtml)) |
| - | * [[bioinformatic_tools:euler|Euler]]((http://nbcr.sdsc.edu/euler/)) | + | * [[archive:bioinformatic_tools:euler|Euler]]((http://nbcr.sdsc.edu/euler/)) |
| - | * [[bioinformatic_tools:euler_sr|Euler-sr]]((http://euler-assembler.ucsd.edu/portal/)) | + | * [[archive:bioinformatic_tools:euler_sr|Euler-sr]]((http://euler-assembler.ucsd.edu/portal/)) |
| - | * [[bioinformatic_tools:mira|MIRA]]((http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page)) | + | * [[archive:bioinformatic_tools:mira|MIRA]]((http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page)) |
| - | * [[bioinformatic_tools:tigr|TIGR]]((ftp://ftp.jcvi.org/pub/software/assembler/)) | + | * [[archive:bioinformatic_tools:tigr|TIGR]]((ftp://ftp.jcvi.org/pub/software/assembler/)) |
| - | * [[bioinformatic_tools:sharcgs|SHARCGS]]((http://sharcgs.molgen.mpg.de/)) | + | * [[archive:bioinformatic_tools:sharcgs|SHARCGS]]((http://sharcgs.molgen.mpg.de/)) |
| - | * [[bioinformatic_tools:ssake|SSAKE]]((http://www.bcgsc.ca/platform/bioinfo/software/ssake)) | + | * [[archive:bioinformatic_tools:ssake|SSAKE]]((http://www.bcgsc.ca/platform/bioinfo/software/ssake)) |
| * [[bioinformatic_tools:staden_gap4|Staden gap4 package]]((http://staden.sourceforge.net/)) | * [[bioinformatic_tools:staden_gap4|Staden gap4 package]]((http://staden.sourceforge.net/)) | ||
| - | * [[bioinformatic_tools:vcake|VCAKE]]((http://sourceforge.net/projects/vcake/)) | + | * [[archive:bioinformatic_tools:vcake|VCAKE]]((http://sourceforge.net/projects/vcake/)) |
| - | * [[bioinformatic_tools:phusion|Phusion]]((http://www.sanger.ac.uk/resources/software/phusion/)) | + | * [[archive:bioinformatic_tools:phusion|Phusion]]((http://www.sanger.ac.uk/resources/software/phusion/)) |
| - | * [[bioinformatic_tools:qsra|QSRA]]((http://qsra.cgrb.oregonstate.edu/)) | + | * [[archive:bioinformatic_tools:qsra|QSRA]]((http://qsra.cgrb.oregonstate.edu/)) |
| - | * [[bioinformatic_tools:Ray|Ray]]((http://denovoassembler.sourceforge.net/)) | + | * [[archive:bioinformatic_tools:ray|Ray]]((http://denovoassembler.sourceforge.net/)) |
| * [[bioinformatic_tools:solid|SOLiD System Tools (Corona_lite, etc)]]((http://solidsoftwaretools.com/gf/)) | * [[bioinformatic_tools:solid|SOLiD System Tools (Corona_lite, etc)]]((http://solidsoftwaretools.com/gf/)) | ||
| - | * [[bioinformatic_tools:SOAPdenovo|SOAPdenovo]]((http://soap.genomics.org.cn/)) | + | * [[archive:bioinformatic_tools:soapdenovo|SOAPdenovo]]((http://soap.genomics.org.cn/)) |
| * [[bioinformatic_tools:Shorty|Shorty]]((http://www.cs.sunysb.edu/~skiena/shorty/)) | * [[bioinformatic_tools:Shorty|Shorty]]((http://www.cs.sunysb.edu/~skiena/shorty/)) | ||
| - | * [[bioinformatic_tools:PRICE|PRICE]]((http://derisilab.ucsf.edu/software/price/index.html/)) | + | * [[archive:bioinformatic_tools:price|PRICE]]((http://derisilab.ucsf.edu/software/price/index.html/)) |
| - | * [[bioinformatic_tools:SGA|Sanger String Graph Assembler]]((http://people.pwf.cam.ac.uk/js779/)) | + | * [[archive:bioinformatic_tools:sga|Sanger String Graph Assembler]]((http://people.pwf.cam.ac.uk/js779/)) |
| - | * [[bioinformatic_tools:pe_assembler|PE-Assembler]]((http://www.comp.nus.edu.sg/~bioinfo/peasm/)) | + | * [[archive:bioinformatic_tools:pe_assembler|PE-Assembler]]((http://www.comp.nus.edu.sg/~bioinfo/peasm/)) |
| == Probably Proprietary Tools and Services == | == Probably Proprietary Tools and Services == | ||
| - | * [[bioinformatic_tools:clc_genomics_workbench|CLC Bio De-novo Assembler]]((http://www.clcbio.com/index.php?id=1413)) | + | * [[archive:bioinformatic_tools:clc_genomics_workbench|CLC Bio De-novo Assembler]]((http://www.clcbio.com/index.php?id=1413)) |
| * [[bioinformatic_tools:codoncode_aligner|CodonCode Aligner]]((http://www.codoncode.com/aligner/)) | * [[bioinformatic_tools:codoncode_aligner|CodonCode Aligner]]((http://www.codoncode.com/aligner/)) | ||
| - | * [[bioinformatic_tools:nextgene|NextGENe]]((http://softgenetics.com/NextGENe.html)) | + | * [[archive:bioinformatic_tools:nextgene|NextGENe]]((http://softgenetics.com/NextGENe.html)) |
| - | * [[bioinformatic_tools:gs_de_novo_assembler|GS De Novo Assembler (aka Newbler)]]((http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp)) | + | * [[archive:bioinformatic_tools:gs_de_novo_assembler|GS De Novo Assembler (aka Newbler)]]((http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp)) |
| * [[bioinformatic_tools:sequencher|Sequencher]]((http://www.genecodes.com/)) | * [[bioinformatic_tools:sequencher|Sequencher]]((http://www.genecodes.com/)) | ||
| * [[bioinformatic_tools:seqman|SeqMan]]((http://www.dnastar.com/t-sub-products-lasergene-seqmanpro.aspx)) | * [[bioinformatic_tools:seqman|SeqMan]]((http://www.dnastar.com/t-sub-products-lasergene-seqmanpro.aspx)) | ||
| Line 62: | Line 62: | ||
| * [[bioinformatic_tools:blat|Blat]] | * [[bioinformatic_tools:blat|Blat]] | ||
| * [[bioinformatic_tools:bowtie|Bowtie]] | * [[bioinformatic_tools:bowtie|Bowtie]] | ||
| - | * [[bioinformatic_tools:bwa|BWA]] | + | * [[archive:bioinformatic_tools:bwa|BWA]] |
| - | * [[bioinformatic_tools:saruman|SARUMAN]] | + | * [[archive:bioinformatic_tools:saruman|SARUMAN]] |
| === Data Transfer Tools === | === Data Transfer Tools === | ||
| - | * [[bioinformatic_tools:udt|UDT]] ((http://udt.sourceforge.net/)) TCP too slow? Transfer data fast with UDT via UDP. | + | * [[archive:bioinformatic_tools:udt|UDT]] ((http://udt.sourceforge.net/)) TCP too slow? Transfer data fast with UDT via UDP. |
| === Visualization Tools === | === Visualization Tools === | ||
| Line 74: | Line 74: | ||
| === Utilities === | === Utilities === | ||
| - | * [[bioinformatic_tools:pluck-scripts|pluck-scripts]] Python scripts written by Kevin Karplus. | + | * [[archive:bioinformatic_tools:pluck-scripts|pluck-scripts]] Python scripts written by Kevin Karplus. |
| * [[computer_resources:rdb|rdb]] Perl scripts for handling tab-separated columns as if they were a relational database. | * [[computer_resources:rdb|rdb]] Perl scripts for handling tab-separated columns as if they were a relational database. | ||
| - | * [[computer_resources:sff_extract|sff_extract]] Python script to extra sff files into standard component files (.fasta, .fasta.qual, .xml) (Overlaps in functionality with the Roche-provided sffinfo tool, which may do a better job of decoding flow-space to base space.) | + | * [[archive:computer_resources:sff_extract|sff_extract]] Python script to extra sff files into standard component files (.fasta, .fasta.qual, .xml) (Overlaps in functionality with the Roche-provided sffinfo tool, which may do a better job of decoding flow-space to base space.) |
| - | * [[computer_resources:illuminaToFastq|illuminaToFastq]] C program to convert the illumina .txt files into fastq format, discarding pairs of reads that do not both pass illumina's quality filter. | + | * [[archive:computer_resources:illuminatofastq|illuminaToFastq]] C program to convert the illumina .txt files into fastq format, discarding pairs of reads that do not both pass illumina's quality filter. |
| - | * [[bioinformatic_tools:samtools|SAM Tools]] A utility for manipulating alignments in SAM format. | + | * [[archive:bioinformatic_tools:samtools|SAM Tools]] A utility for manipulating alignments in SAM format. |
archive/bioinformatic_tools.1436992302.txt.gz · Last modified: 2015/07/15 20:31 by ceisenhart
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
