{"id":7254,"date":"2023-11-21T14:01:53","date_gmt":"2023-11-21T14:01:53","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=7254"},"modified":"2023-11-21T14:02:31","modified_gmt":"2023-11-21T14:02:31","slug":"breseq","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/breseq\/","title":{"rendered":"Breseq"},"content":{"rendered":"

Overview<\/h2>\n

Breseq<\/a> is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes. It is a command line tool implemented in C++ and R.<\/p>\n

Version 0.38.1 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

Breseq is released under the GPL v2 License<\/a>. There are no restrictions on accessing this software on the CSF but all usage must adhere to the license.<\/p>\n

Please cite your usage<\/a> of Breseq.<\/p>\n

Set up procedure<\/h2>\n

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

Load one of the following modulefiles:<\/p>\n

\r\nmodule load apps\/binapps\/breseq\/0.38.1\r\n<\/pre>\n
If you need to use bowtie2 in conjunction with breseq, please see the installed bowtie versions<\/a> on the CSF. You may need to load one of the modulefiles listed there too.<\/p>\n
Running the application<\/h2>\n
Please do not run breseq on the login node to perform computational work. Jobs should be submitted to the compute nodes via batch.<\/p>\n
You can run it on the login nodes to obtain the help text:<\/p>\n
\r\nbreseq --help\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Load the version you require\r\nmodule load apps\/binapps\/breseq\/0.38.1\r\n\r\n# By default breseq will use 1 CPU core, which is correct for a serial job\r\nbreseq arg1 arg2 ... \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
Breseq can be run using multiple CPU cores. This should reduce solution time and also give you access to more memory. Create a jobscript similar to the following:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 8    # Number of cores. Can be 2 -- 32.\r\n\r\n# Load the version you require\r\nmodule load apps\/binapps\/breseq\/0.38.1\r\n\r\n# Breseq uses the -j flag to specify the number of cores to use.\r\n# $NSLOTS will be set automatically to the number given above on the pe line\r\nbreseq -j $NSLOTS arg1 arg2 ... \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
High Memory Jobs<\/h2>\n
If you require more memory for your processing, please see the high memory jobs<\/a> page.<\/p>\n
Further info<\/h2>\n