{"id":145,"date":"2014-01-20T13:42:17","date_gmt":"2014-01-20T13:42:17","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=145"},"modified":"2014-01-20T13:51:44","modified_gmt":"2014-01-20T13:51:44","slug":"bowtie","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/bowtie\/","title":{"rendered":"bowtie"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.<\/p>\n<p>Version 0.12.9 &#038; 1.0.0 binaries are available on the iCSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: <code>$BOWTIE_HOME\/$BOWTIE_VER\/COPYING<\/code><\/p>\n<p>For citation information see the <a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\">Bowtie website<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To use the software you will need to load the modulefile:<\/p>\n<pre class>module load apps\/binapps\/bowtie\/1.0.0<\/pre>\n<pre class>module load apps\/binapps\/bowtie\/0.12.9<\/pre>\n<p>Indexes &#8211; No pre-built indexes have been installed. Users should download and build their own indexes and set the variable BOWTIE_INDEXES on the command line or in .bashrc . For example, in your scratch area:<\/p>\n<pre class=\"in1\">export BOWTIE_INDEXES=$HOME\/scratch\/my_indexes<\/pre>\n<h2>Running the application<\/h2>\n<h3>Examples<\/h3>\n<ul>\n<li>Build the <code>AF293<\/code> reference into the build format <code>contig1.build<\/code>\n<pre>bowtie-build AF293_REF.fasta contig1.build<\/pre>\n<\/li>\n<li>Run bowtie to build a file of reads that don&#8217;t map to contig1 (<code>AF293<\/code>):\n<pre>bowtie -S -q contig1.build C023MABXX_3_5_1.fastq 351.sam --un unmapped351.fastq\r\n<\/pre>\n<\/ul>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/bowtie-bio.sourceforge.net\/manual.shtml\">Bowtie Manual<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. Version 0.12.9 &#038; 1.0.0 binaries are available on the iCSF. Restrictions on use All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: $BOWTIE_HOME\/$BOWTIE_VER\/COPYING For citation information see the Bowtie website. Set up procedure To use the software you will need.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/bowtie\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-145","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/145","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=145"}],"version-history":[{"count":6,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/145\/revisions"}],"predecessor-version":[{"id":160,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/145\/revisions\/160"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=145"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}