bowtie-software
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bowtie-software [2014/10/17 07:51] – joguya | bowtie-software [2014/10/17 08:03] – joguya | ||
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===== 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 2.2.3 ==== | ==== v 2.2.3 ==== | ||
=== 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