Package: capsid
CaPSIDCaPSID(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 LeaderVincent FerrettiDevelopment TeamIvan Borozan, Philippe Laflamme, Shane Wilson, Stuart WattDownloading and using CaPSID is free, if you use CaPSID or its code in your work
please acknowledge CaPSID by referring to its github homepagehttps://github.com/capsid.
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 StartedYou will need a MongoDB database, a Python 2.7 installation and a Java Web Server. For more details, read the wiki:https://github.com/capsid/capsid/wiki/License and CopyrightLicensed under the GNU General Public License, Version 3.0. See LICENSE for more details.Copyright 2011 The Ontario Institute for Cancer Research.AcknowledgementThis project is supported by the Ontario Institute for Cancer Research
(OICR) through funding provided by the government of Ontario, Canada.News1.6.2Release date: 16 July 2014enforce the use of pymongo version==2.81.6.1Release date: 16 September 2014added taxon tables for virusesadded gra (genome relative abundance) calculationsmetrics 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 refspaired reads from the human ref pair-end BAM file are considered valid only if aligned as proper pairschanged the filtering approach from collapsing of FASTQ and filtering to filteringfixed a bug to do with the RAM usage when reading a xeno file during subtraction1.4.3Release date: 2 October 2012Fixes Error message when running subtraction and alignment is not foundMore work on fixing long running queries1.4.2Release date: 2 September 2012Removes MongoKit dependency1.4.1Release date: 4 July 2012Fixes cursor timeout for long running statistics queries1.4.0Release date: 1 June 2012Adds statistics while they are being run rather than all at the endSaves unique id for genes as uid1.3.0Release date: 28 Feb 2012Adds a new field in mapped for AS tagLinks mapped genes to NCBI pageUses max sample coverage for project max coverageAdds timer to wait for file collapsing to finish when intersectingUsing a path/to/file input no longer breaks intersecting1.2.6Release date: 6 Feb 2012Subtraction filters out unmapped when building mapped reads1.2Release date: 20 Jan 2012Utility to create FastQ files from unmapped readsUtility to return intersection of FastQ filesUtility to return filter FastQ filesAdded mapq threshold flag to subtractionGbloader can now load bacteria and fungal genomesSaves genome sequences to database using GridFSReduced memory footprint when calculating statisticsuse subprocesses instead of os.systemmapq scores filter needs to include 0 <= mapq <=3 due to multiple mapping reads1.1Release date: 25 Nov 2011Adds support for pair-end reads1.0.1Release date: 19 Oct 2011Added support for MongoDB authentication1.0Release date: 12 Oct 2011Initial release