capsid 1.2

CaPSID: Computational Pathogen Sequence Identification

CaPSID

CaPSID (Computational Pathogen Sequence IDentification) is a comprehensive open source platform which integrates a high-performance computational pipeline for pathogen sequence identification and characterization in human genomes and transcriptomes together with a scalable results database and a user-friendly web-based software application for managing, querying and visualizing results.

Project Leader Vincent Ferretti Developement Team Ivan Borozan, Philippe Laflamme, Shane Wilson

Getting Started

You will need a MongoDB database, a Python 2.6+ installation and a Java Web Server. For more details, read the wiki:

https://github.com/capsid/capsid/wiki/

License and Copyright

Licensed under the GNU General Public License, Version 3.0. See LICENSE for more details.

Copyright 2011 The Ontario Institute for Cancer Research.

News

1.2

Release date: 20 Jan 2012

• Utility to create FastQ files from unmapped reads

• Utility to return intersection of FastQ files

• Utility to return filter FastQ files

• Added mapq threshold flag to subtraction

• Gbloader can now load bacteria and fungal genomes

• Saves genome sequences to database using GridFS

• Reduced memory footprint when calculating statistics

• use subprocesses instead of os.system

• mapq scores filter needs to include 0 <= mapq <=3 due to multiple mapping reads

1.1

Release date: 25 Nov 2011

• Adds support for pair-end reads

1.0.1

Release date: 19 Oct 2011

• Added support for MongoDB authentication

1.0

Release date: 12 Oct 2011

• Initial release