bowtie-software
Differences
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| bowtie-software [2014/10/17 07:51] – joguya | bowtie-software [2014/10/30 17:01] – [v 2.2.2] joguya | ||
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| ===== Bowtie 1 ===== | ===== Bowtie 1 ===== | ||
| + | ==== v1.0.1 ==== | ||
| + | * Version: 1.0.1 | ||
| + | * Link: http:// | ||
| + | |||
| + | === Usage === | ||
| + | * show all versions of bowtie< | ||
| + | |||
| + | ---------------------------------------------------------------------------------------------- / | ||
| + | bowtie/ | ||
| + | </ | ||
| + | * load a specific version, e.g. v1.1.1: < | ||
| + | * get quick help:< | ||
| + | |||
| ==== v1.1.1 ==== | ==== v1.1.1 ==== | ||
| + | * Version: 1.1.1 | ||
| + | * Added: October, 2014 | ||
| + | * 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 === | === Usage === | ||
| * show all versions of bowtie< | * show all versions of bowtie< | ||
| Line 52: | Line 72: | ||
| ===== Bowtie 2 ===== | ===== 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 3.2 GB. | ||
| + | * Bowtie2 supports gapped, local, and paired-end alignment modes. | ||
| + | ==== v 2.2.2 ==== | ||
| + | * Version 2.2.2 | ||
| + | * Link: http:// | ||
| + | |||
| + | |||
| + | === Usage === | ||
| + | * show all versions of bowtie2< | ||
| + | |||
| + | ---------------------------------------------------------------------------------------------- / | ||
| + | bowtie2/ | ||
| + | </ | ||
| + | * load specific version, e.g. v2.2.2:< | ||
| + | * get help:< | ||
| + | |||
| ==== v 2.2.3 ==== | ==== v 2.2.3 ==== | ||
| + | * Version 2.2.3 | ||
| + | * Added: October, 2014 | ||
| + | * Link: http:// | ||
| + | * 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 === | === Usage === | ||
| + | * show all versions of bowtie2< | ||
| + | ---------------------------------------------------------------------------------------------- / | ||
| + | bowtie2/ | ||
| + | </ | ||
| + | * 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.txt · Last modified: 2020/04/27 11:13 by aorth