bowtie-software
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| bowtie-software [2014/10/30 16:56] – joguya | bowtie-software [2020/04/27 11:13] (current) – aorth | ||
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| ====== Bowtie ====== | ====== Bowtie ====== | ||
| - | * Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). | + | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). |
| - | * For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive. | + | |
| - | * There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp. | + | |
| - | * [[http:// | + | |
| - | ===== Bowtie 1 ===== | + | For reads longer than about 50 bp [[bowtie2-software|Bowtie 2]] is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie |
| - | ==== v1.0.1 ==== | + | |
| - | * Version: 1.0.1 | + | |
| - | * Link: http:// | + | |
| - | === Usage === | + | ===== Information ===== |
| - | * show all versions of bowtie< | + | |
| - | ---------------------------------------------------------------------------------------------- / | + | |
| - | bowtie/ | + | |
| - | </ | + | |
| - | * load a specific version, e.g. v1.1.1: < | + | |
| - | * get quick help:< | + | |
| - | + | ||
| - | ==== v1.1.1 ==== | + | |
| - | | + | |
| * Added: October, 2014 | * Added: October, 2014 | ||
| + | * Updated: April, 2020 | ||
| * Link: http:// | * Link: http:// | ||
| - | * Changelog: | ||
| - | * Fixed a compiling linkage problem related with Mavericks OSX. | ||
| - | * Improved performance for cases where the reference contains ambiguous or masked nucleobases represented by Ns. | ||
| - | * Some minor automatic tests updates. | ||
| - | === Usage === | ||
| - | * show all versions of bowtie< | ||
| - | ---------------------------------------------------------------------------------------------- / | + | ===== Usage ===== |
| - | bowtie/ | + | |
| - | </ | + | |
| - | * load a specific version, e.g. v1.1.1: < | + | |
| - | * get quick help:< | + | |
| - | === Installation === | + | See versions of bowtie |
| - | * bowtie | + | < |
| - | unzip bowtie-1.1.1-linux-x86_64.zip | + | |
| - | sudo mkdir / | + | |
| - | sudo cp -r bowtie-1.1.1/ | + | |
| - | </code> | + | |
| - | * create | + | |
| - | ##################################################################### | + | |
| - | ## | + | |
| - | ## bowtie Modulefile | + | |
| - | ## By James Oguya, j.oguya@cgiar.org | + | |
| - | ## October, 2014 | + | |
| - | ## | + | |
| - | set appname | + | Load one version |
| - | set version | + | < |
| - | set prefix | + | $ bowtie</ |
| - | set exec_prefix | + | |
| - | set url " | + | |
| - | set msg "bowtie | + | |
| - | module-whatis $msg | ||
| - | proc ModulesHelp { } { | + | ===== Installation ====== |
| - | puts stderr " | + | Notes from the sysadmin during installation: |
| - | } | + | |
| - | conflict | + | < |
| - | + | $ wget ' | |
| - | prepend-path | + | $ unzip bowtie-1.2.3-linux-x86_64.zip |
| - | * push the new module using ansible< | + | $ cd bowtie-1.2.3-linux-x86_64 |
| - | + | $ sudo mkdir -p /export/apps/bowtie/1.2.3 | |
| - | + | $ sudo cp -r . /export/ | |
| - | ---- | + | |
| - | + | ||
| - | ===== Bowtie 2 ===== | + | |
| - | * Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. | + | |
| - | * It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. | + | |
| - | * Bowtie2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around | + | |
| - | * Bowtie2 supports gapped, local, and paired-end alignment modes. | + | |
| - | + | ||
| - | ==== v 2.2.3 ==== | + | |
| - | * Version | + | |
| - | * Added: October, 2014 | + | |
| - | * Link: http://bowtie-bio.sourceforge.net/ | + | |
| - | * Changelog: | + | |
| - | * Fixed a bug that made loading an index into memory crash sometimes. | + | |
| - | * Fixed a silent failure to warn the user in case the -x option is missing. | + | |
| - | * Updated al, un, al-conc and un-conc options to avoid confusion in cases where the user does not provide a base file name. | + | |
| - | * Fixed a spurious assert that made bowtie2-inspect debug fail. | + | |
| - | + | ||
| - | === Usage === | + | |
| - | * show all versions of bowtie2< | + | |
| - | + | ||
| - | ---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ---------------------------------------------------------------------------------------------- | + | |
| - | bowtie2/2.1.0 bowtie2/2.2.2 bowtie2/2.2.3 | + | |
| </ | </ | ||
| - | * load specific version, e.g. v2.2.3:< | ||
| - | * get help:< | ||
| - | |||
| - | === Installation === | ||
| - | * bowtie2 is precompiled already, so all you have to do is copy the binaries to export-apps< | ||
| - | unzip bowtie2-2.2.3-linux-x86_64.zip | ||
| - | sudo mkdir / | ||
| - | sudo cp -rv bowtie2-2.2.3/ | ||
| - | |||
| - | * create module file:< | ||
| - | ##################################################################### | ||
| - | ## | ||
| - | ## bowtie2 Modulefile | ||
| - | ## by James Oguya, j.oguya@cgiar.org | ||
| - | ## October, 2014 | ||
| - | ## | ||
| - | |||
| - | set appname | ||
| - | set version | ||
| - | set prefix | ||
| - | set exec_prefix | ||
| - | set url " | ||
| - | set msg " | ||
| - | |||
| - | proc ModulesHelp { } { | ||
| - | puts stderr " | ||
| - | } | ||
| - | |||
| - | module-whatis | ||
| - | conflict | ||
| - | prepend-path | ||
| - | * as always, push to github & let ansible take care of teh rest!< | ||
bowtie-software.1414688182.txt.gz · Last modified: 2014/10/30 16:56 by joguya