LICENSE

TandemTools
Copyright (c) 2020 Saint Petersburg State University

TandemTools is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License, Version 2,
dated June 1991, as published by the Free Software Foundation.

TandemTools 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.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.


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Third-party tools used into TandemTools:

1. TandemTools uses Flye in mapping module and in polishing module.

For more details about Flye please refer to
https://github.com/fenderglass/Flye/ and to the following paper:

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs",
Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8

2. TandemQUAST uses StringDecomposer to partition reads and assemblies into distinct monomers.

For more details about StringDecomposer please refer to
https://github.com/TanyaDvorkina/stringdecomposer

3. TandemTools uses Jellyfish for k-mer counting.

For more details about Jellyfish please refer to
Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Bioinformatics (2011) 27(6): 764-770 doi:10.1093/bioinformatics/btr011

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		    GNU GENERAL PUBLIC LICENSE
		       Version 2, June 1991

 Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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