Software to Support Sperm-Typing for Detecting Recombination Hotspots
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common use autoconf for versioning Nov 6, 2015
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README.md

hotspot - Software to Support Sperm-Typing for Detecting Recombination Hotspots

Linda Odenthal-Hesse, Julien Dutheil, Fabian Klötzl, Bernhard Haubold

GETTING STARTED

To build and install all programs execute the following steps. The first step is not required, if you download the latest release. Please note that libdivsufsort, gsl and tabix are required prerequisites.

autoreconf -i
./configure
make
make install

For extensive installation instructions see the hotspotDoc.pdf.

Usage

Download the example data from our server or via the commandline.

make get-chr19-data-mus

Executing asp

asp -g ./data/mus/genome/ -s ./data/mus/vcf/ ./data/mus/exampleHotSpots19.txt

Executing aso

aso -g ./data/mus/genome/ -s ./data/mus/vcf/ ./data/mus/exampleHotSpots19.txt

Executing Universals in aso

aso -u -g ./data/mus/genome/ -s ./data/mus/vcf/ ./data/mus/exampleHotSpots19.txt

Executing xov

xov ./data/mus/exampleResults.txt

Executing six

six

Testing xov using six

six | xov

License

Copyright (C) 2015, 2018 Bernhard Haubold

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details.

Contact

In case of problems, file a bug or contact us via haubold@evolbio.mpg.de