QUASR

QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include:
duplicate removal
demultiplexing
primer-removal
quality-assurance (QA) graphing
quality control (QC)
consensus-generation
minority-variant determination
minority-variant graphing

The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. Both are written to be as lightweight as possible so they can run with minimal memory-requirements on a desktop or laptop as well as on a compute cluster.

If you have any problems with QUASR, please do contact me at the email address provided in the README.

Project Samples

List of functions performed by the pre-processing quality control (QC) script quality_control.py

List of functions performed by the pre-processing script readset_parser.py

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License

GNU General Public License version 3.0 (GPLv3)

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oid-3316598 Posted 2011-03-30

The entire pipeline is very usefull for data analysis and it very nicely displays everything in well designed graphs. A very good and intuitive approach to getting a feel for what is happening in your sample! A must have for anyone doing NGS data-analysis...

Additional Project Details

Operating Systems

BSD, Linux

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Python

Related Categories

Python Bio-Informatics Software

Registered

2011-03-28

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