CaPSID

CaPSID 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.

Getting Started

You will need a MongoDB database, a Python 2.6+ installation and Apache Tomcat 6+. For more details, read the wiki:

http://wiki.github.com/capsid/capsid/home

What is new in this release:

• Fixes Error message when running subtraction and alignment is not found
• More work on fixing long running queries

What is new in version 1.4.2:

• Removes MongoKit dependency

What is new in version 1.4.1:

• Fixes cursor timeout for long running statistics queries

What is new in version 1.4.0:

• Adds statistics while they are being run rather than all at the end
• Saves unique id for genes as uid

What is new in version 1.2.7:

• Fixes README

What is new in version 1.2.6:

• Subtraction filters out unmapped when building mapped reads

What is new in version 1.2:

• 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

What is new in version 1.1:

• Adds support for pair-end reads

What is new in version 1.0.1:

• Added support for MongoDB authentication

Requirements:

• Python