LICENSE.txt

QUAST: QUality ASsessment Tool for Genome Assemblies
Copyright (c) 2015-2017 Saint Petersburg State University
Copyright (c) 2011-2015 Saint Petersburg Academic University

QUAST 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.

QUAST 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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Main authors:
    Alexey Gurevich
    Vladislav Saveliev
    Alla Mikheenko
    Nikolay Vyahhi
    Glenn Tesler

Other contributors:
    Andrey Prjibelski
    Gleb Valin
    Aleksey Komissarov

Thanks for testing and feedback:
    Irina Vasilinetc
    Dmitry Antipov

Logo design:
    Elena Strelnikova

Contact:
    quast.support@bioinf.spbau.ru
    http://quast.sf.net
    http://quast.bioinf.spbau.ru

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If you use QUAST in your research, please include Gurevich et al., 2013 into your
reference list:

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler,
QUAST: quality assessment tool for genome assemblies,
Bioinformatics (2013) 29 (8): 1072-1075. doi: 10.1093/bioinformatics/btt086
First published online: February 19, 2013

If you use MetaQUAST in your research, please include Mikheenko et al., 2016 into 
your reference list:

Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich,
MetaQUAST: evaluation of metagenome assemblies,
Bioinformatics (2016) 32 (7): 1088-1090. doi: 10.1093/bioinformatics/btv697
First published online: November 26, 2015

If you use Icarus visualizations in your research, please include 
Mikheenko et al., 2016 into your reference list:

Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich,
Icarus: visualizer for de novo assembly evaluation,
Bioinformatics (2016) 32 (21): 3321-3323. doi: 10.1093/bioinformatics/btw379
First published online: July 4, 2016


Third-party tools incorporated into QUAST:

1. QUAST aligns contigs to reference genomes using E-MEM aligner which is an
improvement of a well-known Nucmer aligner from MUMmer package.

For more details about E-MEM please refer to
http://www.csd.uwo.ca/~ilie/E-MEM/ website and to the following paper:

Nilesh Khiste and Lucian Ilie
E-MEM: efficient computation of maximal exact matches for very large genomes.
Bioinformatics (2015), 31(4): 509-14.

For more details about MUMer please refer to
http://mummer.sourceforge.net/ website and to the following paper:

Kurtz, S, Phillippy, A, Delcher, AL, Smoot, M, Shumway, M, Antonescu, C, Salzberg, SL
Versatile and open software for comparing large genomes.
Genome Biol. (2004), 5, 2:R12.

2. GeneMarkS as well as MetaGeneMark and GeneMark-ES gene prediction software
was provided by Mark Borodovsky and Georgia Institute of Technology. 
If you are academic, non-profit institution or U.S. Government agency
please, see License Agreement in the file quast_libs/genemark/linux_64/LICENSE or online at
http://exon.gatech.edu/GeneMark/license_download.cgi. 
If you are not academic, not non-profit institution and not U.S. Government agency, 
you must receive an appropriate license to use GeneMarkS, MetaGeneMark and GeneMark-ES 
in QUAST through Gene Probe, Inc. (http://www.genepro.com/; custserv@genepro.com)

For more details about GeneMarkS please refer to 
http://exon.gatech.edu/GeneMark/genemarks.cgi website and to the following paper:

John Besemer, Alexandre Lomsadze and Mark Borodovsky 
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. 
Implications for finding sequence motifs in regulatory regions. 
Nucleic Acids Research (2001) 29, pp 2607-2618

For more details about GeneMark-ES please refer to 
http://exon.gatech.edu/GeneMark/gmes_instructions.html website and to the following paper:

Alexandre Lomsadze, Vardges Ter-Hovhannisyan, Yury O. Chernoff, and Mark Borodovsky 
Gene identification in novel eukaryotic genomes by self-training algorithm.
Nucleic Acids Research (2005) 33, pp 6494-6506

For more details about MetaGeneMark please refer to 
http://exon.gatech.edu/GeneMark/meta_gmhmmp.cgi website and to the following papers:

Wenhan Zhu, Alex Lomsadze and Mark Borodovsky 
Ab initio gene identification in metagenomic sequences 
Nucleic Acids Research (2010) 38, e132

John Besemer and Mark Borodovsky 
Heuristic approach to deriving models for gene finding 
Nucleic Acids Research (1999) 27, pp 3911-3920

3. Dr. Salzberg kindly agreed to include GAGE scripts as a part of QUAST under GPLv2.
These scripts was also modified by QUAST team. They can be distributed and used in 
QUAST pipeline with current remarks and citation. 
For more details about GAGE please refer to 
http://http://gage.cbcb.umd.edu/data/index.html website and to 
the following paper:

Steven L. Salzberg, Adam M. Phillippy, Aleksey Zimin, Daniela Puiu1, 
Tanja Magoc, Sergey Koren, Todd J. Treangen, Michael C. Schatz, 
Arthur L. Delcher, Michael Roberts, Guillaume Marçais, Mihai Pop and 
James A. Yorke (2011) GAGE: A critical evaluation of genome assemblies and 
assembly algorithms. Genome Res. 22(3): doi:10.1101/gr.131383.111

4. QUAST module contigs_analyzer.py is based on assess_assembly.pl script
which was kindly provided by Plantagora team.
For more details about assess_assembly.pl please refer to 
http://www.plantagora.org website and to the following paper:

Barthelson R, McFarlin AJ, Rounsley SD, Young S (2011) Plantagora: Modeling 
Whole Genome Sequencing and Assembly of Plant Genomes. PLoS ONE 6(12): e28436. 
doi:10.1371/journal.pone.0028436

5. QUAST Gene Finding module uses GlimmerHMM for predicting genes in eukaryoutes.
For more details about GlimmerHMM please refer to
http://cbcb.umd.edu/software/glimmerhmm/ website and to the following paper:

Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM:
two open-source ab initio eukaryotic gene-finders. Bioinformatics. 20(16): 2878-9.

6. MetaQUAST uses BLAST and SILVA 16S rRNA database for predicting content of de novo
metagenomic assemblies. 
Users from NON-ACADEMIC environments can access downloaded SILVA database but only 
for limited/temporary use (only for test purposes). All downloaded files have 
to be deleted latest after 48 hours. Unauthorized usage beyond test purposes is 
strictly prohibited. If you are interested in unlimited usage of the SILVA database 
within a non-academic/commercial environment, please contact contact@arb-silva.de 
for more information. 

For more details about BLAST please refer to
http://blast.ncbi.nlm.nih.gov/Blast.cgi website and to the following paper:

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) 
Basic local alignment search tool. J. Mol. Biol. 215:403-410.

For more details about SILVA please refer to
http://www.arb-silva.de/ website and to the following paper:

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) 
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. 
Nucl. Acids Res. 41 (D1): D590-D596.

7. MetaQUAST uses Krona tools for visualizing dataset taxonomic profile based on
reference genomes found in SILVA database. Please, see License Agreement in the file
quast_libs/kronatools/LICENSE.txt or online at
http://sourceforge.net/p/krona/git/ci/master/tree/KronaTools/LICENSE.txt.

For more details about Krona tools please refer to
http://sourceforge.net/p/krona/home/krona/ website and to the following paper:

Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web
browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.

8. QUAST uses BWA and Sambamba for calculating reads mapping statistics.
For more details about BWA please refer to
https://github.com/lh3/bwa website and to the following preprint:

Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.

For more details about Sambamba please refer to
https://github.com/lomereiter/sambamba website and to the following paper:

A. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins.
Sambamba: fast processing of NGS alignment formats. Bioinformatics, 2015.

9. QUAST Structural Variation Finding module uses Manta.
For more details about Manta please refer to
https://github.com/Illumina/manta website and to the following paper:

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M, Cox A, Kruglyak S, Saunders C.
Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Bioinformatics, 32(8): 1220-1222.

10. Icarus uses Bedtools for calculating read coverage.
For more details about Bedtools please refer to
http://bedtools.readthedocs.io/ website and to the following paper:

Quinlan, AR, Hall, IM (2010). BEDTools: a flexible suite of utilities for comparing 
genomic features. Bioinformatics, 26, 6:841-2.

11. QUAST uses Gnuplot for creating MUMmer alignment dotplot.
For more details about Gnuplot please refer to
http://gnuplot.sourceforge.net/ website and Copyright file under quast_libs/gnuplot/

12. QUAST uses LAP for calculating assembly likelihood scores.
For more details about LAP please refer to
http://assembly-eval.sourceforge.net/ website and to the following paper:

Ghodsi, M., Hill, C. M., Astrovskaya, I., Lin, H., Sommer, D. D., Koren, S., & Pop, M.
De novo likelihood-based measures for comparing genome assemblies.
BMC research notes 6 (2013): 334.

13. QUAST uses Jellyfish for unique k-mers counting.
For more details about Jellyfish please refer to
http://www.genome.umd.edu/jellyfish.html website and to the following paper:

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 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011

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