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
Comments not found