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CaPSID: Computational Pathogen Sequence Identification

Project description


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 Development Team Ivan Borozan, Philippe Laflamme, Shane Wilson, Stuart Watt

Downloading and using CaPSID is free, if you use CaPSID or its code in your work please acknowledge CaPSID by referring to its github homepage This is important for us since obtaining grants is one significant way to fund planning and implementation for our project. Also if you find CaPSID useful in your research feel free to let us know.

Getting Started

You will need a MongoDB database, a Python 2.7 installation and a Java Web Server. For more details, read the wiki:


This project is supported by the Ontario Institute for Cancer Research (OICR) through funding provided by the government of Ontario, Canada.



Release date: 16 July 2014

  • enforce the use of pymongo version==2.8


Release date: 16 September 2014

  • added taxon tables for viruses

  • added gra (genome relative abundance) calculations

  • metrics are now calculated for i) reads aligning to pathogen only (excluding those aligning simultaneously to the human ref (i.e digital subtraction)) and ii) reads aligning simultaneously to both pathogen and human refs

  • paired reads from the human ref pair-end BAM file are considered valid only if aligned as proper pairs

  • changed the filtering approach from collapsing of FASTQ and filtering to filtering

  • fixed a bug to do with the RAM usage when reading a xeno file during subtraction


Release date: 2 October 2012

  • Fixes Error message when running subtraction and alignment is not found

  • More work on fixing long running queries


Release date: 2 September 2012

  • Removes MongoKit dependency


Release date: 4 July 2012

  • Fixes cursor timeout for long running statistics queries


Release date: 1 June 2012

  • Adds statistics while they are being run rather than all at the end

  • Saves unique id for genes as uid


Release date: 28 Feb 2012

  • Adds a new field in mapped for AS tag

  • Links mapped genes to NCBI page

  • Uses max sample coverage for project max coverage

  • Adds timer to wait for file collapsing to finish when intersecting

  • Using a path/to/file input no longer breaks intersecting


Release date: 6 Feb 2012

  • Subtraction filters out unmapped when building mapped reads


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


Release date: 25 Nov 2011

  • Adds support for pair-end reads


Release date: 19 Oct 2011

  • Added support for MongoDB authentication


Release date: 12 Oct 2011

  • Initial release

Project details

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