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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.

Read these first

• Quick Setup
• Installation
• Tutorial

Documentation

• Guide to aligning RNA seq data
• CaPSID's utils howto
• Setting Up User Permissions for a Project
• Creating a Configuration File
• Pipeline Examples
• Release Notes
• Setting up a sharded database