NPG: Short-read sequencing pipeline

These interoperble hosted webservices support our short-read sequencing pipeline enabling automation of the entire instrument platform.

License

These files are part of NPG.

NPG 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 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

[Genome Research Limited]

Pipeline tracking

New sequencing pipeline tracking

An MVC-style application, data model, and web/programmable API in Perl, for tracking runs and related entities performed using the new sequencing technologies (primarily Illumina/Solexa).

cgi-bin/
Basic CGI
data/
TT2 templates, application config file
htdocs/
CSS, javascript, graphics
lib/api/
Web API
lib/controller.pm
Application controller
lib/model/
Data model
lib/view/
Application views
scripts/
Database dumping & access scripts, deployment, examples
t/
Tests!

Downloads

Common modules

New Sequencing common modules

Common modules shared over the different NPG applications

lib/npg_common/
namespace for shared modules
mock/
space for lib/npg_common replacement for Sanger specific modules
t/
Tests!

Downloads

QC application

New sequencing pipeline QC

This is a database backended application for providing statistics that come out of the Illumina/Solexa pipeline process.

This is an MVC-style application in Perl using the ClearPress framework.

cgi-bin/
Basic CGI
data/
TT2 templates, application config file
htdocs/
CSS, javascript, graphics
lib/api/
Web API
lib/controller.pm
Application controller
lib/model/
Data model
lib/view/
Application views
scripts/
Database dumping & access scripts
t/
Tests!

Downloads

Analysis Pipeline

New Sequencing analysis pipeline

A pipeline which runs illumina and in-house post sequencing analysis and qc using lsf.

Requires the pipeline tracking and common modules packages for the main running of the pipeline.

For internal qc, and archival pipelines, it requires the QC application.

bin/
contains the scripts needed to run the pipeline and certain 'functions'
data/config_files
location of the configuration files needed to tell the pipeline locations, lsf queues etc.
lib/npg_pipeline
namespace for the class modules which run the pipeline
t/
Tests!

Downloads

Contacts

* quick link - http://q.sanger.ac.uk/fmumd3dj