MiCall

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

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# MiCall #
## Processing FASTQ data from an Illumina MiSeq ##
[![Code Coverage]][codecov]
[![DOI]][zenodo]

[Code Coverage]: https://codecov.io/github/cfe-lab/MiCall/coverage.svg?branch=master
[codecov]: https://codecov.io/github/cfe-lab/MiCall?branch=master
[DOI]: https://zenodo.org/badge/DOI/10.5281/zenodo.1289989.svg
[zenodo]: https://doi.org/10.5281/zenodo.1289989

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][steps] for details of what the pipeline does.
The [admin] page describes how to look after the pipeline in Kive, and the
[getting started] page describes how to get the docker version set up and run it
on your own data.

[steps]: https://cfe-lab.github.io/MiCall/steps
[admin]: https://cfe-lab.github.io/MiCall/admin
[getting started]: https://cfe-lab.github.io/MiCall/getting_started

## 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][gnu]. The source code for
this program is available from [github.com][github].

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][contact] 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 is distributed under the [Python 3 license][python].

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

Matplotlib is distributed under the [Matplotlib license][matplotlib].

Reportlab is distributed under the BSD license.

Pyyaml and Cutadapt are distributed under the MIT license.

[gnu]: https://www.gnu.org/licenses/
[github]: https://github.com/cfe-lab/MiCall
[contact]: mailto:micalldev@cfenet.ubc.ca
[python]: https://docs.python.org/3/license.html
[matplotlib]: https://matplotlib.org/users/license.html

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