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capsid 1.2

CaPSID: Computational Pathogen Sequence Identification

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Latest Version: 1.2.7

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/

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
 
File Type Py Version Uploaded on Size # downloads
capsid-1.2.tar.gz (md5) Source 2012-01-20 17KB 226