LoFreq 0.6.1 was added to the cluster (05\/12\/2013)<\/p>\n
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.<\/p>\n
http:\/\/sourceforge.net\/p\/lofreq\/wiki\/Home\/<\/a> $ module load apps\/lofreq $ ls $LOFREQDIR $ ls $LOFREQBIN \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n $ module whatis apps\/lofreq Title: LoFreq Name: lofreq Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@85035c8 Builder: root@headnode1.lampredi.cluster.local For further information, execute:<\/p>\n module help apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3<\/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 $ module help apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3<\/p>\n ———– Module Specific Help for ‘apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3’ —————————<\/p>\n ======== LoFreq ======== This module sets up your environment for the use of the ‘lofreq’ >> SYNOPSIS << LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly call low-frequency variants by exploiting base-call quality values. LoFreq has been used to call rare variants in viral and bacterial sequencing datasets and can be used to study mitochondrial heteroplasmy and rare somatic mutations in heterogeneous tumors. LoFreq makes full use of base-call qualities (and versions >=0.5 >> LICENSING << This package is made available subject to the following license(s): BSD License Please refer to the website for further details regarding licensing. >> FURTHER INFORMATION << More information about this software can be found at the website: http:\/\/sourceforge.net\/p\/lofreq\/wiki\/Home\/ For further details regarding this module, including the environment modifications it will apply, execute: module show apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3 >> GET STARTED <<<\/p>\n Please refer to the website for further details on usage of this \u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n $ module show apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3 module-whatis<\/p>\n Title: LoFreq Name: lofreq Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@85035c8 Builder: root@headnode1.lampredi.cluster.local For further information, execute:<\/p>\n module help apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3<\/p>\n module-prereq libs\/gcc\/system \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 LoFreq 0.6.1 was added to the cluster (05\/12\/2013) A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. http:\/\/sourceforge.net\/p\/lofreq\/wiki\/Home\/ \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\/lofreq apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3 | — libs\/gcc\/system | * –> OK | — apps\/python\/2.7.3\/gcc-4.4.6 | | — libs\/gcc\/system … SKIPPED (already loaded) | * –> OK | OK $ ls […]<\/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-326","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\/326","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=326"}],"version-history":[{"count":8,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/326\/revisions"}],"predecessor-version":[{"id":346,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/326\/revisions\/346"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=326"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=326"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=326"}],"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
\napps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\n| — libs\/gcc\/system
\n| * –> OK
\n| — apps\/python\/2.7.3\/gcc-4.4.6
\n| | — libs\/gcc\/system … SKIPPED (already loaded)
\n| * –> OK
\n|
\nOK<\/p>\n
\nbin python<\/p>\n
\nbase_qual_calib_wrapper.sh lofreq_bonf.py lofreq_pileup_summary.py lofreq_snpcaller.py lofreq_varpos_to_vcf.py
\nbwa_unique.sh lofreq_diff.py lofreq_regionbed.py lofreq_uniq_pipeline.py lofreq_version.py
\nlofreq_alnoffset.py lofreq_filter.py lofreq_samtools lofreq_uniq.py<\/p>\n
\napps\/lofreq :<\/p>\n
\nSummary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
\nLicense: BSD License
\nGroup: Bioinformatics
\nURL: http:\/\/sourceforge.net\/p\/lofreq\/wiki\/Home\/<\/p>\n
\nVersion: 0.6.1
\nModule: apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\nModule path: \/opt\/gridware\/etc\/modules\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\nPackage path: \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3<\/p>\n
\nPackage: apps\/lofreq\/0.6.1@18d95c51
\nLast update: 2013-12-05<\/p>\n
\nBuild date: 2013-12-05T16:00:29
\nBuild modules: apps\/python\/2.7.3\/gcc-4.4.6
\nCompiler: compilers\/gcc\/system
\nSystem: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
\nArch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
\nDependencies: libs\/gcc\/system (using: libs\/gcc\/system)
\napps\/python\/2.7.3\/gcc-4.4.6 (using: apps\/python\/2.7.3\/gcc-4.4.6)<\/p>\n
\nfast and sensitive variant-caller for inferring SNVs from
\nhigh-throughput sequencing data
\n=======================<\/p>\n
\napplication. This module sets up version ‘0.6.1’ of the
\napplication.<\/p>\n
\nalso use read mapping qualities) which are usually ignored by other
\nmethods or only used for filtering. It is very sensitive; most
\nnotably, it is able to predict variants below the average base-call
\nquality (i.e. sequencing error rate). Each SNV call is assigned a
\np-value which allows for rigorous false positive control. Even
\nthough it uses no approximations or heuristics, it is very efficient
\ndue to several runtime optimizations. LoFreq is generic and fast
\nenough to be applied to high-coverage data and large genomes. It
\ntakes a minute to analyze Dengue genome sequencing data with nearly
\n4000X coverage, roughly one hour to call SNVs on a 600X coverage
\nE.coli genome and 1.5 hours to run on a 100X coverage human exome
\ndataset.<\/p>\n
\npackage.<\/p>\n
\n——————————————————————-
\n\/opt\/gridware\/etc\/modules\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3:<\/p>\n
\nSummary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
\nLicense: BSD License
\nGroup: Bioinformatics
\nURL: http:\/\/sourceforge.net\/p\/lofreq\/wiki\/Home\/<\/p>\n
\nVersion: 0.6.1
\nModule: apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\nModule path: \/opt\/gridware\/etc\/modules\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\nPackage path: \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3<\/p>\n
\nPackage: apps\/lofreq\/0.6.1@18d95c51
\nLast update: 2013-12-05<\/p>\n
\nBuild date: 2013-12-05T16:00:29
\nBuild modules: apps\/python\/2.7.3\/gcc-4.4.6
\nCompiler: compilers\/gcc\/system
\nSystem: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
\nArch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
\nDependencies: libs\/gcc\/system (using: libs\/gcc\/system)
\napps\/python\/2.7.3\/gcc-4.4.6 (using: apps\/python\/2.7.3\/gcc-4.4.6)<\/p>\n
\nmodule-prereq apps\/python\/2.7.3\/gcc-4.4.6
\nmodule-conflict apps\/lofreq
\nsetenv LOFREQDIR \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3
\nsetenv LOFREQBIN \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3\/bin
\nsetenv LOFREQPYTHON \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3\/python
\nprepend-path PATH \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3\/bin
\nprepend-path PYTHONPATH \/opt\/gridware\/pkg\/apps\/lofreq\/0.6.1\/gcc-4.4.6+python-2.7.3\/python\/lib\/python2.7\/site-packages<\/p>\n
\nigm-lampredi-users@ncl.ac.uk<\/p>\n
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"