LICENSE.txt

QUAST: QUality ASsessment Tool for Genome Assemblies
Copyright (c) 2022-2024 Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), HZI
Copyright (c) 2015-2022 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.

-------------------------------------------------------------------------------

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

Other contributors:
    Andrey Prjibelski
    Gleb Valin
    Aleksey Komissarov
    Pascal Hirsch

Thanks for testing and feedback:
    Irina Vasilinetc
    Dmitry Antipov

Logo design:
    Elena Strelnikova

Contact:
    alexey.gurevich@helmholtz-hips.de
    http://quast.sf.net

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If you use the latest QUAST version or WebQUAST, please include our latest paper,
Mikheenko et al., 2023, into your reference list:

Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich,
WebQUAST: online evaluation of genome assemblies,
Nucleic Acids Research (2023) 51 (W1): W601–W606. doi: 10.1093/nar/gkad406
First published online: May 17, 2023

If you use QUAST v5.0.* or QUAST-LG in your research, please include
Mikheenko et al., 2018 into your reference list:

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

If you use QUAST v4.* or 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

If you use QUAST v3.* or 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 QUAST v1.* or v2.* in your research or want to cite QUAST software in general,
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


Third-party tools incorporated into QUAST:

1. QUAST uses Minimap2 for aligning long reads and contigs to reference genomes.

For more details about Minimap2 please refer to
https://github.com/lh3/minimap2 and to the following paper:

Li H. (2017) Minimap2: fast pairwise alignment for long nucleotide sequences.
Bioinformatics (2018). doi: 10.1093/bioinformatics/bty191
First published online: May 10, 2018

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. 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

4. QUAST Gene Finding module uses GlimmerHMM for predicting genes in eukaryotes.
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.

5. 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.

6. 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.

7. 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.
https://arxiv.org/abs/1303.3997

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 Jun 15;31(12):2032-4. doi: 10.1093/bioinformatics/btv098.
Epub 2015 Feb 19.

8. QUAST Structural Variation Finding module uses GRIDSS.
For more details about GRIDSS please refer to
https://github.com/PapenfussLab/gridss website and to the following paper:

D. L. Cameron, J. Schroeder, J. S. Penington, H. Do, R. Molania, A. Dobrovic,
T. P. Speed and A. T. Papenfuss. GRIDSS: sensitive and specific genomic rearrangement
detection using positional de Bruijn graph assembly.
Genome Res. 2017 Dec;27(12):2050-2060. doi: 10.1101/gr.222109.117. Epub 2017 Nov 2.

9. 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.

10. QUAST-LG uses KMC for unique k-mers counting.
For more details about KMC please refer to
http://sun.aei.polsl.pl/kmc website and to the following paper:

Kokot, M., Dlugosz, M., Deorowicz, S., KMC 3: counting and manipulating k-mer statistics.
Bioinformatics. 2017 Sep 1;33(17):2759-2761. doi: 10.1093/bioinformatics/btx304.

11. QUAST uses Barrnap for ribosomal RNA genes prediction.
For more details about Barrnap please refer to
https://github.com/tseemann/barrnap website.

12. QUAST uses Circos for visualizing all assembly data in a circular layout
(Circos needs to be installed and added to the PATH environment variable).
For more details about Circos please refer to
http://www.circos.ca website and to the following paper:

Krzywinski, M. et al., Circos: an Information Aesthetic for Comparative Genomics.
Genome Res (2009) 19:1639-1645

13. QUAST-LG uses Red for detecting repeats (for upper bound assembly construction).
For more details about Red please refer to
http://toolsmith.ens.utulsa.edu website and to the following paper:

Hani Z. Girgis. Red: an intelligent, rapid, accurate tool for detecting repeats
de-novo on the genomic scale. BMC Bioinformatics (2015) 16:227

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