FASTQC 0.10.1, a quality control tool for high throughput sequence data, has been added to the cluster (24\/02\/2014)<\/p>\n
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.<\/p>\n
The main functions of FastQC are<\/p>\n
\n
- Import of data from BAM, SAM or FastQ files (any variant)<\/li>\n
- Providing a quick overview to tell you in which areas there may be problems<\/li>\n
- Summary graphs and tables to quickly assess your data<\/li>\n
- Export of results to an HTML based permanent report<\/li>\n
- Offline operation to allow automated generation of reports without running the interactive application<\/li>\n<\/ul>\n<\/blockquote>\n
http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/a>
\n
\n---------------------------------------------------------------------------------<\/code><\/p>\n$ module load apps\/fastqc<\/p>\n
apps\/fastqc\/0.10.1\/noarch<\/p>\n
|<\/p>\n
OK<\/p>\n
$ ls $FASTQCDIR<\/p>\n
app\u00a0 bin\u00a0 doc<\/p>\n
$ fastqc –version<\/p>\n
FastQC v0.10.1<\/p>\n
———————————————————————————<\/p>\n
\n$ module whatis apps\/fastqc<\/p>\n
apps\/fastqc\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 :<\/p>\n
<\/p>\n
Title: FastQC<\/p>\n
Summary: A quality control tool for high throughput sequence data<\/p>\n
License: GPLv3+<\/p>\n
Group: Bioinformatics<\/p>\n
URL: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/p>\n
<\/p>\n
Name: fastqc<\/p>\n
Version: 0.10.1<\/p>\n
Module: apps\/fastqc\/0.10.1\/noarch<\/p>\n
Module path: \/opt\/gridware\/etc\/modules\/apps\/fastqc\/0.10.1\/noarch<\/p>\n
Package path: \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch<\/p>\n
<\/p>\n
Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0d67d87<\/p>\n
Package: apps\/fastqc\/0.10.1@0380e731<\/p>\n
Last update: 2012-10-31<\/p>\n
<\/p>\n
Builder: root@headnode1.lampredi.cluster.local<\/p>\n
Build date: 2014-02-24T10:41:03<\/p>\n
Compiler: N\/A<\/p>\n
<\/p>\n
For further information, execute:<\/p>\n
module help apps\/fastqc\/0.10.1\/noarch<\/p>\n<\/div>\n
<\/p>\n
———————————————————————————<\/p>\n
\n$ module help apps\/fastqc\/0.10.1\/noarch<\/p>\n
<\/p>\n
———– Module Specific Help for ‘apps\/fastqc\/0.10.1\/noarch’ —————————<\/p>\n
<\/p>\n
<\/p>\n
======== FastQC ========<\/p>\n
A quality control tool for high throughput sequence data<\/p>\n
=======================<\/p>\n
<\/p>\n
This module sets up your environment for the use of the ‘fastqc’<\/p>\n
application. This module sets up version ‘0.10.1’ of the<\/p>\n
application.<\/p>\n
<\/p>\n
<\/p>\n
>> SYNOPSIS <<<\/p>\n
<\/p>\n
FastQC aims to provide a simple way to do some quality control<\/p>\n
checks on raw sequence data coming from high throughput sequencing<\/p>\n
pipelines. It provides a modular set of analyses which you can use<\/p>\n
to give a quick impression of whether your data has any problems of<\/p>\n
which you should be aware before doing any further analysis.<\/p>\n
<\/p>\n
The main functions of FastQC are:<\/p>\n
<\/p>\n
* Import of data from BAM, SAM or FastQ files (any variant)<\/p>\n
* Providing a quick overview to tell you in which areas there may<\/p>\n
be problems<\/p>\n
* Summary graphs and tables to quickly assess your data<\/p>\n
* Export of results to an HTML based permanent report<\/p>\n
* Offline operation to allow automated generation of reports<\/p>\n
without running the interactive application<\/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
GPLv3+<\/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
http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/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\/fastqc\/0.10.1\/noarch<\/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<\/div>\n
<\/div>\n———————————————————————————<\/div>\n\n<\/div>\n\n$ module show apps\/fastqc\/0.10.1\/noarch<\/p>\n
<\/p>\n
\/opt\/gridware\/etc\/modules\/apps\/fastqc\/0.10.1\/noarch:<\/p>\n
<\/p>\n
module-whatis<\/p>\n
<\/p>\n
Title: FastQC<\/p>\n
Summary: A quality control tool for high throughput sequence data<\/p>\n
License: GPLv3+<\/p>\n
Group: Bioinformatics<\/p>\n
URL: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/p>\n
<\/p>\n
Name: fastqc<\/p>\n
Version: 0.10.1<\/p>\n
Module: apps\/fastqc\/0.10.1\/noarch<\/p>\n
Module path: \/opt\/gridware\/etc\/modules\/apps\/fastqc\/0.10.1\/noarch<\/p>\n
Package path: \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch<\/p>\n
<\/p>\n
Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@0d67d87<\/p>\n
Package: apps\/fastqc\/0.10.1@0380e731<\/p>\n
Last update: 2012-10-31<\/p>\n
<\/p>\n
Builder: root@headnode1.lampredi.cluster.local<\/p>\n
Build date: 2014-02-24T10:41:03<\/p>\n
Compiler: N\/A<\/p>\n
<\/p>\n
<\/p>\n
For further information, execute:<\/p>\n
<\/p>\n
module help apps\/fastqc\/0.10.1\/noarch<\/p>\n
<\/p>\n
module-conflict apps\/fastqc<\/p>\n
setenv FASTQCDIR \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch<\/p>\n
setenv FASTQCBIN \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch\/bin<\/p>\n
setenv FASTQCAPP \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch\/app<\/p>\n
setenv FASTQCDOC \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch\/doc<\/p>\n
prepend-path PATH \/opt\/gridware\/pkg\/apps\/fastqc\/0.10.1\/noarch\/bin<\/p>\n<\/div>\n<\/div>\n
<\/div>\n\n———————————————————————————<\/p>\n
\nLampredi HPC
\nigm-lampredi-users@ncl.ac.uk<\/p>\nIGM IT
\nigmithelp@ncl.ac.uk
\nx8625<\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"FASTQC 0.10.1, a quality control tool for high throughput sequence data, has been added to the cluster (24\/02\/2014) FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a […]<\/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-320","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\/320","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=320"}],"version-history":[{"count":6,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/320\/revisions"}],"predecessor-version":[{"id":359,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/320\/revisions\/359"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=320"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=320"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=320"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}