CoNvex Gap-cost alignMents for Long Reads (ngmlr<\/a>) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes<\/p>\n The application is written in C++ and can be used in batch or interactively (via the qrsh command).<\/p>\n There are no restrictions on using this software on the CSF. The application is released under the MIT license.<\/p>\n To access the software you must first load the modulefile:<\/p>\n Please do not run canu on the login node. Jobs should be submitted to the compute nodes via batch or run interactively via the qrsh command.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using:<\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n FastQC can be run interactively but this must not<\/strong> be run on the login node. Instead you must schedule an interactive session on a compute node. Use the following commands (after loading the modulefile):<\/p>\n This will only run when a free core is available on one of the interactive nodes. If no free resources are available you will be asked to try again later.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes The application is written in C++ and can be used in batch or interactively (via the qrsh command). Version 0.2.6-beta is installed on the CSF. Restrictions on use There are no restrictions on using this software on the CSF. The application is released under the MIT license. Set up procedure To.. Read more »<\/a><\/p>\n","protected":false},"author":24,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4565","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4565","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\/24"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4565"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4565\/revisions"}],"predecessor-version":[{"id":4566,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4565\/revisions\/4566"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=4565"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
module load apps\/gcc\/ngmlr\/0.2.6-beta\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\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\ngmlr [-t <threads>] -r <reference> -q <reads> [-o <output>]\r\n\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Interactive use of the GUI<\/h3>\n
qrsh -l inter -l short -V canu\r\n<\/pre>\n
Further info<\/h2>\n
\n
ngmlr -help\r\n<\/pre>\n<\/li>\n<\/ul>\n
Updates<\/h2>\n