MitoSeek has been updated to version 1.2, as of 24\/02\/2014<\/p>\n
This is a\u00a0software tool to reliably and easily extract mitochondrial genome information from exome sequencing data.<\/p>\n
https:\/\/github.com\/riverlee\/MitoSeek apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n | — libs\/gcc\/system<\/p>\n |\u00a0 \u00a0 * –> OK<\/p>\n | — apps\/perl\/5.16.1\/gcc-4.4.6<\/p>\n |\u00a0 \u00a0 | — libs\/gcc\/system … SKIPPED (already loaded)<\/p>\n |\u00a0 \u00a0 * –> OK<\/p>\n | — apps\/samtools\/0.1.18\/gcc-4.4.6<\/p>\n |\u00a0 \u00a0 | — libs\/gcc\/system … SKIPPED (already loaded)<\/p>\n |\u00a0 \u00a0 * –> OK<\/p>\n |<\/p>\n OK<\/p>\n <\/p>\n \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n <\/p>\n $ module whatis apps\/mitoseek\/1.2<\/p>\n apps\/mitoseek\/1.2\u00a0 \u00a0 :<\/p>\n <\/p>\n Title: MitoSeek<\/p>\n Summary: Extraction of mitochondrial genome information from exome sequencing data<\/p>\n License: GPLv2<\/p>\n Group: Bioinformatics<\/p>\n URL: https:\/\/github.com\/riverlee\/MitoSeek<\/p>\n <\/p>\n Name: mitoseek<\/p>\n Version: 1.2<\/p>\n Module: apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n Module path: \/opt\/gridware\/etc\/modules\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n Package path: \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n <\/p>\n Repository: file:\/opt\/gridware\/etc\/repos\/local<\/p>\n Package: apps\/mitoseek\/1.2@6ea5eade<\/p>\n Last update: 2014-02-24<\/p>\n <\/p>\n Builder: root@headnode1.lampredi.cluster.local<\/p>\n Build date: 2014-02-24T11:08:18<\/p>\n Build modules: apps\/perl\/5.16.1\/gcc-4.4.6, apps\/samtools\/0.1.18\/gcc-4.4.6, apps\/cpanminus\/1.5017\/noarch<\/p>\n Compiler: compilers\/gcc\/system<\/p>\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n apps\/perl\/5.16.1\/gcc-4.4.6 (using: apps\/perl\/5.16.1\/gcc-4.4.6)<\/p>\n apps\/samtools\/0.1.18\/gcc-4.4.6 (using: apps\/samtools\/0.1.18\/gcc-4.4.6)<\/p>\n <\/p>\n For further information, execute:<\/p>\n <\/p>\n module help apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n <\/p>\n $ module help apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n <\/p>\n ———– Module Specific Help for ‘apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18’ —————————<\/p>\n <\/p>\n <\/p>\n ======== MitoSeek ========<\/p>\n Extraction of mitochondrial genome information from exome<\/p>\n sequencing data<\/p>\n =========================<\/p>\n <\/p>\n This module sets up your environment for the use of the ‘mitoseek’<\/p>\n application. This module sets up version ‘1.2’ of the<\/p>\n application.<\/p>\n <\/p>\n <\/p>\n >> SYNOPSIS <<<\/p>\n <\/p>\n MitoSeek is an open-source software tool to reliably and easily<\/p>\n extract mitochondrial genome information from exome sequencing data.<\/p>\n MitoSeek evaluates mitochondrial genome alignment quality, estimates<\/p>\n relative mitochondrial copy numbers, and detects heteroplasmy,<\/p>\n somatic mutation, and structural variance of the mitochondrial<\/p>\n genome.<\/p>\n <\/p>\n <\/p>\n >> LICENSING <<<\/p>\n <\/p>\n This package is made available subject to the following license(s):<\/p>\n <\/p>\n GPLv2<\/p>\n <\/p>\n Please refer to the website for further details regarding licensing.<\/p>\n <\/p>\n <\/p>\n >> FURTHER INFORMATION <<<\/p>\n <\/p>\n More information about this software can be found at the website:<\/p>\n <\/p>\n https:\/\/github.com\/riverlee\/MitoSeek<\/p>\n <\/p>\n For further details regarding this module, including the environment<\/p>\n modifications it will apply, execute:<\/p>\n <\/p>\n module show apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n <\/p>\n <\/p>\n >> GET STARTED <<<\/p>\n <\/p>\n Please refer to the website for further details on usage of this<\/p>\n package.<\/p>\n \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n <\/p>\n $ module show apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n ——————————————————————-<\/p>\n \/opt\/gridware\/etc\/modules\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18:<\/p>\n <\/p>\n module-whatis<\/p>\n <\/p>\n Title: MitoSeek<\/p>\n Summary: Extraction of mitochondrial genome information from exome sequencing data<\/p>\n License: GPLv2<\/p>\n Group: Bioinformatics<\/p>\n URL: https:\/\/github.com\/riverlee\/MitoSeek<\/p>\n <\/p>\n Name: mitoseek<\/p>\n Version: 1.2<\/p>\n Module: apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n Module path: \/opt\/gridware\/etc\/modules\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n Package path: \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n <\/p>\n Repository: file:\/opt\/gridware\/etc\/repos\/local<\/p>\n Package: apps\/mitoseek\/1.2@6ea5eade<\/p>\n Last update: 2014-02-24<\/p>\n <\/p>\n Builder: root@headnode1.lampredi.cluster.local<\/p>\n Build date: 2014-02-24T11:08:18<\/p>\n Build modules: apps\/perl\/5.16.1\/gcc-4.4.6, apps\/samtools\/0.1.18\/gcc-4.4.6, apps\/cpanminus\/1.5017\/noarch<\/p>\n Compiler: compilers\/gcc\/system<\/p>\n System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<\/p>\n Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)<\/p>\n Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n apps\/perl\/5.16.1\/gcc-4.4.6 (using: apps\/perl\/5.16.1\/gcc-4.4.6)<\/p>\n apps\/samtools\/0.1.18\/gcc-4.4.6 (using: apps\/samtools\/0.1.18\/gcc-4.4.6)<\/p>\n <\/p>\n For further information, execute:<\/p>\n <\/p>\n module help apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n <\/p>\n module-prereq libs\/gcc\/system<\/p>\n module-prereq apps\/perl\/5.16.1\/gcc-4.4.6<\/p>\n module-prereq apps\/samtools\/0.1.18\/gcc-4.4.6<\/p>\n module-conflict apps\/mitoseek<\/p>\n setenv MITOSEEKDIR \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18<\/p>\n setenv MITOSEEKBIN \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/bin<\/p>\n setenv MITOSEEKDOC \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/doc<\/p>\n prepend-path PERL5LIB \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/perl\/lib\/perl5<\/p>\n prepend-path MANPATH \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/perl\/man<\/p>\n prepend-path PATH \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/bin<\/p>\n prepend-path PATH \/opt\/gridware\/pkg\/apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18\/perl\/bin<\/p>\n \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n Lampredi HPC IGM IT <\/p>\n","protected":false},"excerpt":{"rendered":" MitoSeek has been updated to version 1.2, as of 24\/02\/2014 This is a\u00a0software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. https:\/\/github.com\/riverlee\/MitoSeek \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014- $ module load apps\/mitoseek\/1.2 apps\/mitoseek\/1.2\/gcc-4.4.6+perl-5.16.1+samtools-0.1.18 | — libs\/gcc\/system |\u00a0 \u00a0 * –> OK | — apps\/perl\/5.16.1\/gcc-4.4.6 |\u00a0 \u00a0 | — libs\/gcc\/system … SKIPPED (already loaded) |\u00a0 \u00a0 […]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[11,10,9,21],"class_list":["post-334","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-cluster","tag-hpc","tag-lampredi","tag-lampredi2","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/334","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=334"}],"version-history":[{"count":8,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/334\/revisions"}],"predecessor-version":[{"id":368,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/334\/revisions\/368"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=334"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=334"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=334"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\n
\n\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/code><\/p>\n$ module load apps\/mitoseek\/1.2<\/pre>\n
\nigm-lampredi-users@ncl.ac.uk<\/p>\n
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n