RADcap: software for sequence capture based RADseq

Release v1.0.0. (Changelog)

Author:Brant C. Faircloth
Date:29 May 2018 18:55 UTC (+0000)
Copyright:This documentation is available under a Creative Commons (CC-BY) license.

radcap is a software package that was developed for analyzing data collected from RADseq loci using the RADcap approach (see Hoffberg et al. 2016 and References for additional information).

Contributions

radcap is open-source (see License) and we welcome contributions from anyone who is interested. Please make a pull request on github. The issue tracker for radcap is also available on github.

Issues

If you have an issue, please ensure that you are experiencing this issue on a supported OS (see Installation) using the conda installation of radcap. If possible, please submit a test case demonstrating the issue and indicate which platform and the git checkout and/or radcap version you are using.

Guide

Purpose

Who wrote this?

This documentation was written primarily by Brant Faircloth (http://faircloth-lab.org). Brant is also responsible for the development of most of the radcap code. Bugs within the code are usually his.

You can find additional authors and contributors in the Attributions section.

How do I report bugs?

To report a bug, please post an issue to https://github.com/faircloth-lab/radcap/issues. Please also ensure that you are using one of the “supported” platforms:

  • Apple OSX 10.9.x
  • CentOS 6.x
  • Ubuntu 14.04 LTS

and that you have installed radcap and dependencies using conda as described in the Installation section.

Installation

More soon.

Project info

Citing

If you use the radcap code in any form, please cite the following manuscript (which is “in review”):

[SH2016]Hoffberg S, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn RC. 2016. Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap). bioRxiv. doi:10.1101/044651.

Please also cite the github repository:

[BCF2016]Faircloth BC. RADcap software. https://github.com/faircloth-lab/radcap.

References

License

Documentation

The documentation for radcap is available under a CC-BY (2.0) license. This license gives you permission to copy, distribute, and trasmit the work as well as to adapt the work or use this work for commercial purposes, under the condition that you must attribute the work to the author(s).

If you use this documentation or the radcap software for your own research, please cite both the software and Hoffberg et al. 2016. See the Citing section for more detail.

Software

Copyright (c) 2016, Brant C. Faircloth All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  • Neither the name of the University of California, Los Angeles nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Changelog

v1.0 (April 2016)

  • initial release

Attributions

A number of people have worked on different aspects of the radcap approach, including creating the laboratory methods to collect the data and the computational methods to analyze the data. Below, we have identified a list of approximately which people/groups did what.

Wrote the code

Contributed to the code

Funding

Primary Sources

The National Science Foundation (NSF) has supported a large portion of our work. The specific programs and proposal identifiers are below:

Secondary Sources

We have also received funding for computational support from and/or materials from the following organizations:

Acknowledgements

We thank the following people, each of whom made contributions ensuring the success of our work. These include:

  • Todd Pierson
  • Kerin Bentley
  • Natalia Bayona