pandaseq is a program to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases.<\/p>\n
Version 2.8 is installed on the CSF.<\/p>\n
This program is free software: you can redistribute it and\/or modify
\n it under the terms of the GNU General Public License as published by
\n the Free Software Foundation, either version 3 of the License, or
\n (at your option) any later version.<\/p>\n
To access the software you must first load the modulefile:<\/p>\n
\r\nmodule load apps\/gcc\/pandaseq\/2.8\r\n<\/pre>\nRunning the application<\/h2>\n
Please do not run pandaseq on the login node. Jobs should be submitted to the compute nodes via batch.<\/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#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\npandaseq arg1 arg2 > out.log\r\n<\/pre>\nSubmit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\nwhere 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#$ -S \/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. 2-24 permitted. Runs on a single compute node.\r\n\r\n# $NSLOTS is automatically set to the number of cores requested above\r\npandaseq -T $NSLOTS arg1 arg2 > out.log\r\n<\/pre>\nSubmit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\nwhere scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n
\n
- pandaseq source website<\/a><\/li>\n<\/ul>\n
Updates<\/h2>\n
None.<\/p>\n","protected":false},"excerpt":{"rendered":"
Overview pandaseq is a program to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. Version 2.8 is installed on the CSF. Restrictions on use This program is free software: you can redistribute it and\/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Set up procedure To.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2497","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2497","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=2497"}],"version-history":[{"count":12,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2497\/revisions"}],"predecessor-version":[{"id":2988,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/2497\/revisions\/2988"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=2497"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}