LICENSE

AGB: Assembly Graph Browser
Copyright (c) 2018 Saint Petersburg State University

AGB 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.

AGB 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 AGB:

1. AGB uses GfaPy to parse GFA files.

For more details about GfaPy please refer to
https://github.com/ggonnella/gfapy and to the following paper:

Giorgio Gonnella and Stefan Kurtz "GfaPy: a flexible and extensible software library for handling sequence graphs in Python",
Bioinformatics (2017) btx398 https://doi.org/10.1093/bioinformatics/btx398

2. AGB uses Networkx-METIS to partition large assembly graphs.

For more details about Networkx-METIS please refer to
https://github.com/networkx/networkx-metis

3. AGB uses d3-graphviz for creating interactive graph visualization.

For more details about d3-graphviz please refer to
https://github.com/magjac/d3-graphviz

4. AGB uses QUAST-LG for detecting assembly errors.

For more details about QUAST-LG please refer to
https://github.com/ablab/quast and to the following paper:

Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich,
Versatile genome assembly evaluation with QUAST-LG,
Bioinformatics (2018) 34 (13): i142-i150. doi: 10.1093/bioinformatics/bty266
First published online: June 27, 2018


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