nasa · bnovak32 · Aug 15, 2025 · Feb 8, 2024 · Feb 8, 2024 · Feb 8, 2024
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina"]
+	path = Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina
+	url = https://github.com/nasa/GeneLab_AmpliconSeq_Workflow
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software.md b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software.md
diff --git a/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/DECIPHER_gpl-3.0.pdf b/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/DECIPHER_gpl-3.0.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/DESeq2_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/DESeq2_LICENSE.pdf
diff --git a/..._and_Metagenomics_3rd_Party_Software_Licenses/The_BIOM_Format_License_biom_format.org.pdf b/..._and_Metagenomics_3rd_Party_Software_Licenses/The_BIOM_Format_License_biom_format.org.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/VSEARCH_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/VSEARCH_LICENSE.pdf
diff --git a/...ty_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/colorbrewer_LICENSE.pdf b/...ty_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/colorbrewer_LICENSE.pdf
diff --git a/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/cutadapt_LICENSE.pdf b/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/cutadapt_LICENSE.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/dada2_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/dada2_LICENSE.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/dplyr_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/dplyr_LICENSE.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/ggrepel_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/ggrepel_LICENSE.pdf
diff --git a/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/phyloseq_LICENSE.pdf b/...Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/phyloseq_LICENSE.pdf
diff --git a/...arty_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/tidyverse_LICENSE.pdf b/...arty_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/tidyverse_LICENSE.pdf
diff --git a/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/vegan_LICENSE.pdf b/3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/vegan_LICENSE.pdf
diff --git a/3rd_Party_Licenses/Metagenomics_3rd_Party_Software.md b/3rd_Party_Licenses/Metagenomics_3rd_Party_Software.md
@@ -0,0 +1,24 @@
+## The NASA GeneLab [Metagenomics](../Metagenomics) Processing Pipelines software 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](Metagenomics_3rd_Party_Software_Licenses/FASTQC_LICENSE.pdf)|[https://github.com/s-andrews/FastQC/blob/master/LICENSE](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](Metagenomics_3rd_Party_Software_Licenses/MultiQC_LICENSE.pdf)|[https://github.com/ewels/MultiQC/blob/master/LICENSE](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.|
+|bbduk|[BBTools Copyright (c) 2014, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.](Metagenomics_3rd_Party_Software_Licenses/bbduk_license.pdf)|[https://github.com/BioInfoTools/BBMap/blob/a9ceda047a7c918dc090de0fdbf6f924292d4a1f/license.txt](https://github.com/BioInfoTools/BBMap/blob/a9ceda047a7c918dc090de0fdbf6f924292d4a1f/license.txt)|BBTools Copyright (c) 2014, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.|
+|megahit|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/megahit_LICENSE.pdf)|[https://github.com/voutcn/megahit/blob/master/LICENSE](https://github.com/voutcn/megahit/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.|
+|bit|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/bit_LICENSE.pdf)|[https://github.com/AstrobioMike/bioinf_tools/blob/master/LICENSE](https://github.com/AstrobioMike/bioinf_tools/blob/master/LICENSE)|Copyright (C) 2007 Free Software Foundation, Inc. <https://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](Metagenomics_3rd_Party_Software_Licenses/bowtie2_LICENSE.pdf)|[https://github.com/BenLangmead/bowtie2/blob/master/LICENSE](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.|
+|samtools|[The MIT/Expat License Copyright (C) 2008-2020 Genome Research Ltd.](Metagenomics_3rd_Party_Software_Licenses/samtools_LICENSE.pdf)|[https://github.com/samtools/samtools/blob/develop/LICENSE](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:|
+|prodigal|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/Prodigal_LICENSE.pdf)|[https://github.com/hyattpd/Prodigal/blob/GoogleImport/LICENSE](https://github.com/hyattpd/Prodigal/blob/GoogleImport/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.|
+|KOFamScan|[MIT License Copyright (c) 2019 Takuya Aramaki](Metagenomics_3rd_Party_Software_Licenses/kofam_scan_LICENSE.pdf)|[https://github.com/takaram/kofam_scan/blob/master/LICENSE.txt](https://github.com/takaram/kofam_scan/blob/master/LICENSE.txt)|Copyright (c) 2019 Takuya Aramaki 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:|
+|CAT|[The MIT License (MIT) Copyright (c) 2019 Universiteit Utrecht](Metagenomics_3rd_Party_Software_Licenses/CAT_LICENSE.pdf)|[https://github.com/dutilh/CAT/blob/master/LICENSE.md](https://github.com/dutilh/CAT/blob/master/LICENSE.md)|Copyright (c) 2019 Universiteit Utrecht 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:|
+|Metabat2|[MetaBAT (2014-075), The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.](Metagenomics_3rd_Party_Software_Licenses/MetaBAT_license.pdf)|[https://bitbucket.org/berkeleylab/metabat/src/master/license.txt](https://bitbucket.org/berkeleylab/metabat/src/master/license.txt)|MetaBAT (2014-075), The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.|
+|checkm|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/CheckM_LICENSE.pdf)|[https://github.com/Ecogenomics/CheckM/blob/master/LICENSE](https://github.com/Ecogenomics/CheckM/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.|
+|gtdbtk|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/GTDBTk_LICENSE.pdf)|[https://github.com/Ecogenomics/GTDBTk/blob/master/LICENSE](https://github.com/Ecogenomics/GTDBTk/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.|
+|KEGGDecoder|[The MIT License (MIT) Copyright (c) 2019 Benjamin Tully](Metagenomics_3rd_Party_Software_Licenses/KEGGDecoder_LICENSE.pdf)|[https://github.com/bjtully/BioData/blob/master/LICENSE](https://github.com/bjtully/BioData/blob/master/LICENSE) | Copyright (c) 2019 Benjamin Tully 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:|
+|HUMAnN3|[The HUMAnN software is licensed under the MIT license. Copyright (c) 2014 Harvard School of Public Health](Metagenomics_3rd_Party_Software_Licenses/HUMAnN_LICENSE.pdf)|[https://github.com/biobakery/humann/blob/master/LICENSE](https://github.com/biobakery/humann/blob/master/LICENSE)|Copyright (c) 2014 Harvard School of Public Health 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:|
+|MetaPhlAn3|[The MIT License (MIT) Copyright (c) 2015, Duy Tin Truong, Nicola Segata and Curtis Huttenhower](Metagenomics_3rd_Party_Software_Licenses/MetaPhlAn3_license.pdf)|[https://github.com/biobakery/MetaPhlAn/blob/3.0/license.txt](https://github.com/biobakery/MetaPhlAn/blob/3.0/license.txt)|Copyright (c) 2015, Duy Tin Truong, Nicola Segata and Curtis Huttenhower|
+|kraken2|[The MIT License (MIT) Copyright (c) 2017-2018 Derrick Wood](Metagenomics_3rd_Party_Software_Licenses/kraken2_LICENSE.pdf)|[https://github.com/DerrickWood/kraken2/blob/master/LICENSE](https://github.com/DerrickWood/kraken2/blob/master/LICENSE)|Copyright (c) 2017-2021 Derrick Wood 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:|
+|Snakemake|[The MIT License (MIT) Copyright (c) 2012-2019 Johannes Köster](Metagenomics_3rd_Party_Software_Licenses/License_Snakemake_6.7.0_documentation.pdf)|[https://snakemake.readthedocs.io/en/stable/project_info/license.html](https://snakemake.readthedocs.io/en/stable/project_info/license.html)|Copyright (c) 2012-2019 Johannes Köster <[email protected]> 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:|
+|genelab-utils|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/genelab-utils_LICENSE.pdf)|[https://github.com/AstrobioMike/GeneLab-utils/blob/main/LICENSE](https://github.com/AstrobioMike/GeneLab-utils/blob/main/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.|
+|R|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991, and Version 3, 29 June 2007](Metagenomics_3rd_Party_Software_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf)|[https://www.r-project.org/Licenses/](https://www.r-project.org/Licenses/)|Version 2: 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.; Version 3: 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.|
diff --git a/...d_Party_Software_Licenses/CAT_LICENSE.pdf → ...d_Party_Software_Licenses/CAT_LICENSE.pdf b/...d_Party_Software_Licenses/CAT_LICENSE.pdf → ...d_Party_Software_Licenses/CAT_LICENSE.pdf
diff --git a/...arty_Software_Licenses/CheckM_LICENSE.pdf → ...arty_Software_Licenses/CheckM_LICENSE.pdf b/...arty_Software_Licenses/CheckM_LICENSE.pdf → ...arty_Software_Licenses/CheckM_LICENSE.pdf
diff --git a/...arty_Software_Licenses/FASTQC_LICENSE.pdf → ...arty_Software_Licenses/FASTQC_LICENSE.pdf b/...arty_Software_Licenses/FASTQC_LICENSE.pdf → ...arty_Software_Licenses/FASTQC_LICENSE.pdf
diff --git a/...arty_Software_Licenses/GTDBTk_LICENSE.pdf → ...arty_Software_Licenses/GTDBTk_LICENSE.pdf b/...arty_Software_Licenses/GTDBTk_LICENSE.pdf → ...arty_Software_Licenses/GTDBTk_LICENSE.pdf
diff --git a/...arty_Software_Licenses/HUMAnN_LICENSE.pdf → ...arty_Software_Licenses/HUMAnN_LICENSE.pdf b/...arty_Software_Licenses/HUMAnN_LICENSE.pdf → ...arty_Software_Licenses/HUMAnN_LICENSE.pdf
diff --git a/...Software_Licenses/KEGGDecoder_LICENSE.pdf → ...Software_Licenses/KEGGDecoder_LICENSE.pdf b/...Software_Licenses/KEGGDecoder_LICENSE.pdf → ...Software_Licenses/KEGGDecoder_LICENSE.pdf
diff --git a/...License_Snakemake_6.7.0_documentation.pdf → ...License_Snakemake_6.7.0_documentation.pdf b/...License_Snakemake_6.7.0_documentation.pdf → ...License_Snakemake_6.7.0_documentation.pdf
diff --git a/...rty_Software_Licenses/MetaBAT_license.pdf → ...rty_Software_Licenses/MetaBAT_license.pdf b/...rty_Software_Licenses/MetaBAT_license.pdf → ...rty_Software_Licenses/MetaBAT_license.pdf
diff --git a/..._Software_Licenses/MetaPhlAn3_license.pdf → ..._Software_Licenses/MetaPhlAn3_license.pdf b/..._Software_Licenses/MetaPhlAn3_license.pdf → ..._Software_Licenses/MetaPhlAn3_license.pdf
diff --git a/...rty_Software_Licenses/MultiQC_LICENSE.pdf → ...rty_Software_Licenses/MultiQC_LICENSE.pdf b/...rty_Software_Licenses/MultiQC_LICENSE.pdf → ...rty_Software_Licenses/MultiQC_LICENSE.pdf
diff --git a/...ty_Software_Licenses/Prodigal_LICENSE.pdf → ...ty_Software_Licenses/Prodigal_LICENSE.pdf b/...ty_Software_Licenses/Prodigal_LICENSE.pdf → ...ty_Software_Licenses/Prodigal_LICENSE.pdf
diff --git a/...e_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf → ...e_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf b/...e_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf → ...e_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf
diff --git a/...Party_Software_Licenses/bbduk_license.pdf → ...Party_Software_Licenses/bbduk_license.pdf b/...Party_Software_Licenses/bbduk_license.pdf → ...Party_Software_Licenses/bbduk_license.pdf
diff --git a/...d_Party_Software_Licenses/bit_LICENSE.pdf → ...d_Party_Software_Licenses/bit_LICENSE.pdf b/...d_Party_Software_Licenses/bit_LICENSE.pdf → ...d_Party_Software_Licenses/bit_LICENSE.pdf
diff --git a/...rty_Software_Licenses/bowtie2_LICENSE.pdf → ...rty_Software_Licenses/bowtie2_LICENSE.pdf b/...rty_Software_Licenses/bowtie2_LICENSE.pdf → ...rty_Software_Licenses/bowtie2_LICENSE.pdf
diff --git a/...ftware_Licenses/genelab-utils_LICENSE.pdf → ...ftware_Licenses/genelab-utils_LICENSE.pdf b/...ftware_Licenses/genelab-utils_LICENSE.pdf → ...ftware_Licenses/genelab-utils_LICENSE.pdf
diff --git a/..._Software_Licenses/kofam_scan_LICENSE.pdf → ..._Software_Licenses/kofam_scan_LICENSE.pdf b/..._Software_Licenses/kofam_scan_LICENSE.pdf → ..._Software_Licenses/kofam_scan_LICENSE.pdf
diff --git a/...rty_Software_Licenses/kraken2_LICENSE.pdf → ...rty_Software_Licenses/kraken2_LICENSE.pdf b/...rty_Software_Licenses/kraken2_LICENSE.pdf → ...rty_Software_Licenses/kraken2_LICENSE.pdf
diff --git a/...rty_Software_Licenses/megahit_LICENSE.pdf → ...rty_Software_Licenses/megahit_LICENSE.pdf b/...rty_Software_Licenses/megahit_LICENSE.pdf → ...rty_Software_Licenses/megahit_LICENSE.pdf
diff --git a/...ty_Software_Licenses/samtools_LICENSE.pdf → ...ty_Software_Licenses/samtools_LICENSE.pdf b/...ty_Software_Licenses/samtools_LICENSE.pdf → ...ty_Software_Licenses/samtools_LICENSE.pdf
diff --git a/3rd_Party_Licenses/README.md b/3rd_Party_Licenses/README.md
@@ -0,0 +1,10 @@
+## The NASA GeneLab Processing Pipelines utilize 3rd party Open Source software as indicated:
+
+| Assay Type                     | 3rd Party Software Table | 3rd Party Software Licenses |
+|:-------------------------------|:-------------------------|:----------------------------|
+| Amplicon Sequencing            | [Amplicon 3rd Party Software](https://github.com/nasa/GeneLab_AmpliconSeq_Workflow/tree/main/License/3rd_Party_Licenses/README.md) | [Amplicon 3rd Party Licenses](https://github.com/nasa/GeneLab_AmpliconSeq_Workflow/tree/main/License/3rd_Party_Licenses) |
+| Metagenomics                   | [Metagenomics 3rd Party Software](./Metagenomics_3rd_Party_Software.md) | [Metagenomics 3rd Party Licenses](./Metagenomics_3rd_Party_Software_Licenses/) |
+| Methylation Sequencing         | [Methyl-Seq 3rd Party Software](./Methyl-Seq_3rd_Party_Software.md) | [Methyl-Seq 3rd Party Licenses](./Methyl-Seq_3rd_Party_Software_Licenses/) |
+| Microarray - Affymetrix        | [Microarray Affymetrix 3rd Party Software](./Microarray_Affymetrix_3rd_Party_Software.md) | [Microarray Affymetrix 3rd Party Licenses](./Microarray_Affymetrix_3rd_Party_Software_Licenses/) | 
+| Microarray - Agilent 1-channel | [Microarray Agilent 1-channel 3rd Party Software](./Microarray_Agilent_1_Channel_3rd_Party_Software.md) | [Microarray Affymetrix 3rd Party Licenses](./Microarray_Agilent_1_Channel_3rd_Party_Software_Licenses/) | 
+| (bulk) RNAseq                  | [RNASeq 3rd Party Software](./RNAseq_3rd_Party_Software.md) | [RNAseq 3rd Party Licenses](./RNAseq_3rd_Party_Software_Licenses/) |
diff --git a/Amplicon/454-and-IonTorrent/README.md b/Amplicon/454-and-IonTorrent/README.md
@@ -7,7 +7,7 @@
 --- 
 
 <p align="center">
-<a href="../images/GL-amplicon-overview.pdf"><img src="../images/GL-amplicon-overview.png"></a>
+<a href="../images/GL-amplicon-subwayplot.pdf"><img src="../images/GL-amplicon-subwayplot.png"></a>
 </p>
 
 ---
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,7 +7,7 @@ @@
     ---
     <p align="center">
-    <a href="../images/GL-amplicon-overview.pdf"><img src="../images/GL-amplicon-overview.png"></a>
+    <a href="../images/GL-amplicon-subwayplot.pdf"><img src="../images/GL-amplicon-subwayplot.png"></a>
     </p>
     ---
@@ Expand Down @@