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The Clear BSD License (BSD 3-Clause Clear License)
Copyright (c) 2020-2021 Medical University of Innsbruck
contributors: Dietmar Rieder, Georgios Fotakis, Francesca Finotello
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted
(subject to the limitations in the disclaimer below) provided that the following conditions
are met:
Redistributions of source code must retain the above copyright notice, this list of conditions
and the following disclaimer. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the documentation and/or other
materials provided with the distribution. Neither the name of Medical University of Innsbruck
nor the names of its contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS LICENSE.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS
OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Licenses for Tools used by nextNEOpi:
-------------------------------------
nextNEOpi uses a variety of other tools which each have their own license restrictions.
The user is aware that nextNEOpi will install and use conda environments and/or Singularity
images that are automatically downloaded from public accessible software repositories.
By using nextNEOpi, either standalone or using its Singularity image, the user implicitly
accepts the license terms of the underlying tools used.
By using the standalone IEDB software installed in the nextNEOpi Singularity images, the user also
implicitly accepts the IEDB license terms.
IEDB (Immune Epitope Database)
Website: https://www.iedb.org
Citation: Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A,
Peters B. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2018 Oct 24.
doi: 10.1093/nar/gky1006. [Epub ahead of print] PubMed PMID: 30357391.
License: Non-Profit OSL 3.0
By using the IEDB software, you are consenting to be bound by and become a “Licensee” for the use
of IEDB tools and are consenting to the terms and conditions of the Non-Profit Open Software License
(“Non-Profit OSL”) version 3.0.
Please read these two license agreements here [1] before proceeding. If you do not agree to all of the
terms of these two agreements, you must not install or use the product. Companies (for-profit entities)
interested in downloading the command-line versions of the IEDB tools or running the entire analysis
resource locally, should contact IEDB (license@iedb.org) for details on licensing options.
[1]: http://tools.iedb.org/mhci/download/
MHCflurry
Website: http://openvax.github.io/mhcflurry/
GitHub: https://github.com/openvax/mhcflurry
Citation: T. J. O’Donnell, A. Rubinsteyn, M. Bonsack, A. B. Riemer, U. Laserson, and J. Hammerbacher,
“MHCflurry: Open-Source Class I MHC Binding Affinity Prediction,” Cell Systems, 2018.
doi: https://doi.org/10.1016/j.cels.2018.05.014. PubMed PMID: 29960884.
License: Apache License 2.0
MHCnuggets
Website: https://karchinlab.org/apps/appMHCnuggets.html
GitHub: https://github.com/KarchinLab/mhcnuggets-2.0
Citation: Bhattacharya R, Sivakumar A, Tokheim C, Beleva Guthrie V, Anagnostou V, Velculescu VE,
Karchin R (2017)
Evaluation of machine learning methods to predict peptide binding to MHC Class I proteins.
Submitted [bioRxiv preprint].
License: Apache License 2.0
NetChop
Website: http://www.cbs.dtu.dk/services/NetChop/
Citation: The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained
from improved predictions of proteasomal cleavage. M. Nielsen, C. Lundegaard, O. Lund,
and C. Kesmir. Immunogenetics., 57(1-2):33-41, 2005. PubMed PMID: 11983929.
License: Academic License
NetMHCstabpan
Website: http://www.cbs.dtu.dk/services/NetMHCstabpan/
Citation: Pan-specific prediction of peptide-MHC-I complex stability; a correlate of T cell
immunogenicity. Michael Rasmussen, Emilio Fenoy, Mikkel Harndahl, Anne Bregnballe
Kristensen, Ida Kallehauge Nielsen, Morten Nielsen, Soren Buus.
J Immunol. 2016 Aug 15;197(4):1517-24.
doi: https://doi.org/10.4049/jimmunol.1600582. PubMed PMID: 27402703.
License: Academic License
Vaxrank
Website: https://github.com/openvax/vaxrank
Citation: Rubinsteyn, A., Hodes, I., Kodysh, J., & Hammerbacher, J. (2017).
Vaxrank: a computational tool for designing personalized cancer vaccines.
bioRxiv, 142919.
License: Apache License 2.0
GATK
Website: https://github.com/broadinstitute/gatk, https://gatk.broadinstitute.org/
Citation: Van der Auwera GA & O'Connor BD. (2020). Genomics in the Cloud: Using Docker,
GATK, and WDL in Terra (1st Edition). O'Reilly Media.
License: Apache License 2.0
VarScan2
Website: https://dkoboldt.github.io/varscan/
Citation: VarScan 2: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin,
L., Miller, C., Mardis, E., Ding, L., & Wilson, R. (2012).
VarScan 2: Somatic mutation and copy number alteration discovery in cancer
by exome sequencing Genome Research DOI: 10.1101/gr.129684.111
Strekla2
Website: https://github.com/Illumina/strelka
Citation: Kim, S., Scheffler, K. et al. (2018) Strelka2: fast and accurate calling
of germline and somatic variants. Nature Methods, 15, 591-594.
doi:10.1038/s41592-018-0051-x
License: GPLv3
Manta
Website: https://github.com/Illumina/manta
Citation: Chen, X. et al. (2016) Manta: rapid detection of structural variants
and indels for germline and cancer sequencing applications.
Bioinformatics, 32, 1220-1222. doi:10.1093/bioinformatics/btv710
License: GPLv3
CNVkit
Website: https://github.com/etal/cnvkit
Citation: Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: Genome-Wide
Copy Number Detection and Visualization from Targeted DNA Sequencing.
PLoS Comput Biol. 2016 Apr 21;12(4):e1004873.
doi: 10.1371/journal.pcbi.1004873. PMID: 27100738; PMCID: PMC4839673.
License: Apache License 2.0
Fastqc
Website: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
License: GPLv3
Fastp
Website: https://github.com/OpenGene/fastp
Citation: Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast
all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17,
1 September 2018, Pages i884–i890,
https://doi.org/10.1093/bioinformatics/bty560
License: MIT License
BWA
Website: http://bio-bwa.sourceforge.net/
Citation: Li H. and Durbin R. (2009) Fast and accurate short read alignment
with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
[PMID: 19451168]
License: GPLv3
samtools/htslib
Website: http://www.htslib.org/
Citation: Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield,
Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham,
Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10,
Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
License: The MIT/Expat License
sambamba
Website: https://lomereiter.github.io/sambamba/
Citation: Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing
of NGS alignment formats. Bioinformatics. 2015 Jun 15;31(12):2032-4.
doi: 10.1093/bioinformatics/btv098. Epub 2015 Feb 19. PMID: 25697820;
PMCID: PMC4765878.
License: GPLv2+
bam-readcount
Website: https://www.crick.ac.uk/research/labs/peter-van-loo/software
License: MIT License
VEP
Website: https://www.ensembl.org/info/docs/tools/vep/index.html
Citation: McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
The Ensembl Variant Effect Predictor. Genome Biology Jun 6;17(1):122. (2016)
doi:10.1186/s13059-016-0974-4
License: Apache License 2.0
OptiType:
Website: https://github.com/FRED-2/OptiType
Citation: Szolek, A, Schubert, B, Mohr, C, Sturm, M, Feldhahn, M, and Kohlbacher, O (2014).
OptiType: precision HLA typing from next-generation sequencing data
Bioinformatics, 30(23):3310-6.
License: BSD 3-Clause "New" or "Revised" License
Sequenza
Website: https://sequenzatools.bitbucket.io/
Citation: F. Favero, T. Joshi,A. M. Marquard, N. J. Birkbak, M. Krzystanek, Q. Li, Z. Szallasi,
and A. C. Eklund. “Sequenza: allele-specific copy number and mutation profiles from
tumor sequencing data”. Annals of Oncology, 2015, vol. 26, issue 1, 64-70.
License: GPLv3
alleleCount
Website: https://github.com/cancerit/alleleCount
License: GNU Affero General Public License
GBM
Website: https://github.com/vincentlaboratories/neoag/
Citation: Smith CC, Chai S, Washington AR, Lee SJ, Landoni E, Field K, Garness J, Bixby LM,
Selitsky SR, Parker JS, Savoldo B, Serody JS, Vincent BG. Machine-Learning
Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes.
Cancer Immunol Res. 2019 Oct;7(10):1591-1604. doi: 10.1158/2326-6066.CIR-19-0155.
Epub 2019 Sep 12. PMID: 31515258; PMCID: PMC6774822.
License: https://github.com/vincentlaboratories/neoag/raw/master/LICENSE.txt
ASCAT
Website: https://www.crick.ac.uk/research/labs/peter-van-loo/software
Citation: Ross EM, Haase K, Van Loo P, Markowetz F. Allele-specific multi-sample copy number
segmentation in ASCAT. Bioinformatics. 2020 May 25:btaa538.
doi: 10.1093/bioinformatics/btaa538. Epub ahead of print. PMID: 32449758.
mixcr
Website: https://github.com/milaboratory/mixcr/
Citation: Dmitriy A. Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar
Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software
for comprehensive adaptive immunity profiling."
Nature methods 12, no. 5 (2015): 380-381.
License: https://github.com/milaboratory/mixcr/blob/develop/LICENSE
MixMHC2pred
Website: https://github.com/GfellerLab/MixMHC2pred
Citation: Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif
deconvolution of immunopeptidomes. Nat. Biotechnol. 37, 1283–1286 (2019).
License: Academic (https://github.com/GfellerLab/MixMHC2pred/blob/master/License.pdf)
Yara
Website: https://github.com/seqan/seqan/tree/master/apps/yara
Citation: Siragusa, E., Weese D., and Reinert, K. (2013). Fast and accurate read mapping with
approximate seeds and multiple backtracking. Nucleic Acids Research, 2013, 1–8.
License: BSD 3-Clause License