Difference between revisions of "Bowtie2"

Latest revision as of 14:48, 14 December 2022

Description

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. Bowtie is a part of the Tuxedo suite.

Note: If you are using bowtie or bowtie2 we installed you do not need to specify the path, only the database name. If you are using some other software and must specify the full path use /data/reference/bowtie2. If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes as an argument to the bowtie2 command.

Environment Modules

Run module spider bowtie2 to find out what environment modules are available for this application.

System Variables

HPC_BOWTIE2_DIR - installation directory
HPC_BOWTIE2_BIN - executable directory
HPC_BOWTIE2_DOC - documents directory
HPC_BOWTIE2_EX - examples directory
HPC_BOWTIE2_SCR - scripts directory
BOWTIE2_INDEXES - pre-built index files directory

Additional Information

Note: If your data is compressed your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.

@@ Line 1: / Line 1: @@
 __NOTOC____NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
 {|
 <!--Main settings - REQUIRED-->
@@ Line 17: / Line 17: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-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.
+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. Bowtie is a part of the [[Tuxedo]] suite.
-Bowtie is a part of the [[Tuxedo]] suite.
+;Note:If you are using bowtie or bowtie2 we installed you do '''not''' need to specify the path, only the database name. If you are using some other software and must specify the full path use <code>/data/reference/bowtie2</code>. If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes as an argument to the bowtie2 command.
-HPC pre-built Bowtie2 Indexes are located in ''/scratch/lfs/bio/reference/bowtie2''. They should be available for bowtie use automatically. If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes as an argument to the bowtie2 command.
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-[[Modules|modules documentation]]
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-*{{#var:app}} -loads the default Bowtie2 version
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_BOWTIE2_BIN - executable directory
 * HPC_BOWTIE2_DOC - documents directory
@@ Line 36: / Line 31: @@
 * HPC_BOWTIE2_SCR - scripts directory
 * BOWTIE2_INDEXES - pre-built index files directory
-<code>/scratch/lfs/bio/reference/bowtie2</code>
 <!--Additional-->
 {{#if: {{#var: exe}}|==Additional Information==
-Note: If your data is compressed your job script should add another ppn to accommodate the external gzip process that bowtie will run. To be safe, add another ppn in any case.
+Note: If your data is compressed your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.
 |}}
 {{#if: {{#var: conf}}|==Configuration==