Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
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README.md

MiCall

Processing FASTQ data from an Illumina MiSeq

Maps all the reads from a sample against a set of reference sequences, then stitches all the reads into consensus sequences and coverage maps.

A monitoring system regularly checks the file system for unprocessed runs, transfers FASTQ.gz files to the cluster and executes the pipeline.

See the list of steps and files for details of what the pipeline does. The admin page describes how to look after the pipeline.

Dual Licensing

Copyright (C) 2016, University of British Columbia

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, visit gnu.org. The source code for this program is available from github.com.

The program is also available for a fee under a more permissive license. For example, if you want to run a changed version of the program on a network server without publishing the changed source code, contact us about purchasing a license.

Third Party Components

MiCall makes use of several open-source tools. Here is a list of tools with their licenses.

Requests is distributed under the Apache 2.0 license.

Python 3.4 is distributed under the Python 3.4 license.

Bowtie2 and Python-Levenshtein are distributed under the GNU General Public License (GPL).

Matplotlib is distributed under the Matplotlib license.

Reportlab is distributed under the BSD license.

Pyyaml and Cutadapt are distributed under the MIT license.