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Methyl-Seq_3rd_Party_Software.md

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The NASA GeneLab Methyl-Seq Processing Pipeline and workflow also makes use of the following 3rd party Open Source software:

3rd Party Software Name License License URL Copyright Notice
FastQC GNU GENERAL PUBLIC LICENSE Version 2, June 1991 https://github.com/s-andrews/FastQC/blob/master/LICENSE Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
MultiQC GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 https://github.com/ewels/MultiQC/blob/master/LICENSE Copyright (C) 2007 Free Software Foundation, Inc http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Cutadapt Copyright (c) 2010-2020 Marcel Martin https://github.com/marcelm/cutadapt/blob/main/LICENSE Copyright (c) 2010-2020 Marcel Martin marcel.martin@scilifelab.se Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
TrimGalore GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 https://github.com/FelixKrueger/TrimGalore/blob/master/LICENSE Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Bismark GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 https://github.com/FelixKrueger/Bismark/blob/master/license.txt Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
bowtie2 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 https://github.com/BenLangmead/bowtie2/blob/master/LICENSE Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
hisat2 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 https://github.com/DaehwanKimLab/hisat2/blob/master/LICENSE Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
samtools The MIT/Expat License Copyright (C) 2008-2020 Genome Research Ltd. https://github.com/samtools/samtools/blob/develop/LICENSE Copyright (C) 2008-2021 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
Qualimap GNU GENERAL PUBLIC LICENSE Version 2, June 1991 https://bitbucket.org/kokonech/qualimap/src/master/LICENSE Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
MethylKit Artistic 2.0 LICENSE Copyright (c) 2000-2006 https://bioconductor.org/packages/release/bioc/html/methylKit.html Copyright (c) 2000-2006, The Perl Foundation. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
tidyverse MIT Licence Copyright (c) 2021 https://tidyverse.tidyverse.org/LICENSE.html MIT License Copyright (c) 2021 tidyverse authors
genomation Artistic 2.0 LICENSE Copyright (c) 2000-2006 https://bioconductor.org/packages/release/bioc/html/genomation.html Copyright (c) 2000-2006, The Perl Foundation. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Nextflow Apache License Version 2.0, January 2004 https://github.com/nextflow-io/nextflow/blob/master/COPYING Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form.