{"id":1235,"date":"2014-01-20T10:37:37","date_gmt":"2014-01-20T10:37:37","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1235"},"modified":"2018-06-26T16:14:41","modified_gmt":"2018-06-26T16:14:41","slug":"bwa","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/bwa\/","title":{"rendered":"BWA"},"content":{"rendered":"

Overview<\/h2>\n

BWA<\/a> (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. There are three algorithms implemented – BWA-backtrack, BWA-SW and BWA-MEM – see the BWA website<\/a> for advice on which to use.<\/p>\n

Versions 0.7.15, 0.7.5a and 0.7.17 are installed on the CSF. They were compiled with gcc 4.7.0.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license<\/a> and all usage must adhere to that license.<\/p>\n

Please cite your usage of this software as detailed on the BWA website<\/a>.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one<\/em> of the following the modulefiles:<\/p>\n

\r\nmodule load apps\/gcc\/bwa\/0.7.17\r\nmodule load apps\/gcc\/bwa\/0.7.15\r\nmodule load apps\/gcc\/bwa\/0.7.5a\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run BWA on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
A full description of all of the BWA commands and flags accepted by the application is beyond the scope of this web-page.<\/p>\n
However, you may<\/em> run the following command on the login node to see a list of flag \/ args that the application will accept. These should be used in your jobscript:<\/p>\n
\r\nman bwa\r\n\r\n(press 'space' to page down through the help text, q to quit)\r\n<\/pre>\n
You may also run the following command on the login node to see a summary of commands and flags accepted by the application:<\/p>\n
\r\nbwa\r\n<\/pre>\n
To see the help text for a specific bwa command<\/em>, run:<\/p>\n
\r\nbwa command<\/em>\r\n<\/pre>\n
For example:<\/p>\n
\r\nbwa fastmap\r\n<\/pre>\n
You must check<\/strong> whether the command you are using accepts a flag to specify the number of threads (cores) to use. This should then be applied to the command-line in your jobscript.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# These commands will only use one core\r\nbwa index args...<\/em>\r\nbwa samse args...<\/em>\r\nbwa sampe args...<\/em>\r\n\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores to use (can be 2 -- 24)\r\n\r\n# $NSLOTS is automatically set to the number of cores specified above\r\n\r\n# These commands can be run using multiple cores\r\nbwa mem -t $NSLOTS args...<\/em>\r\nbwa aln -t $NSLOTS args...<\/em>\r\nbwa bwasw -t $NSLOTS args...<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n