Merge pull request #1098 from StaPH-B/cjk-issues-1072-and-824

closes issues 1072 and 824 - referencing publications

README.md

@@ -212,7 +212,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [medaka](https://hub.docker.com/r/staphb/medaka) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) | <ul><li>[0.8.1](./medaka/0.8.1/)</li><li>[1.0.1](./medaka/1.0.1/)</li><li>[1.2.0](./medaka/1.2.0/)</li><li>[2.0.0](./medaka/2.0.0/)</li><li>[2.0.1](./medaka/2.0.1/)</li></ul> | https://github.com/nanoporetech/medaka |
 | [metaphlan](https://hub.docker.com/r/staphb/metaphlan) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) | <ul><li>[3.0.3-no-db (no database)](./metaphlan/3.0.3-no-db/)</li><li> [3.0.3 (~3GB db)](./metaphlan/3.0.3/)</li><li>[4.1.0](./metaphlan/4.1.0/) (no database)</li><li>[4.1.1](./metaphlan/4.1.1/) (no database)</li></ul> | https://github.com/biobakery/MetaPhlAn |
 | [MIDAS](https://hub.docker.com/r/staphb/midas) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) | <ul><li>1.3.2 (no database)</li> | https://github.com/snayfach/MIDAS |
-| [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li><li>[2.26](./minimap2/2.26)</li><li>[2.27](./minimap2/2.27/)</li>li>[2.28](./minimap2/2.28/)</li></ul> | https://github.com/lh3/minimap2 |
+| [minimap2](https://hub.docker.com/r/staphb/minimap2) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) | <ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li><li>[2.26](./minimap2/2.26)</li><li>[2.27](./minimap2/2.27/)</li><li>[2.28](./minimap2/2.28/)</li></ul> | https://github.com/lh3/minimap2 |
 | [minipolish](https://hub.docker.com/r/staphb/minipolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) | <ul><li>0.1.3</li></ul> | https://github.com/rrwick/Minipolish |
 | [mlst](https://hub.docker.com/r/staphb/mlst) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) | <ul><li>2.16.2</li><li>2.17.6</li><li>2.19.0</li><li>2.22.0</li><li>2.22.1</li><li>2.23.0</li><li>[2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)</li><li>[2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)</li><li>[2.23.0-2024-01 (databases updated Jan 2024)](mlst/2.23.0-2024-01/)</li><li>[2.23.0-2024-03 (databases updated March 2024)](mlst/2.23.0-2024-03/)</li></ul> | https://github.com/tseemann/mlst |
 | [Mugsy](https://hub.docker.com/r/staphb/mugsy) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) | <ul><li>1r2.3</li></ul> | http://mugsy.sourceforge.net/ |

fastani/1.33-RGDv2/README.md

@@ -6,7 +6,7 @@ Full documentation: https://github.com/ParBLiSS/FastANI
 
 FastANI was developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes.
 
-This docker image contains the Reference Genome Database version 2 (RGDv2) from the Enteric Diseases Laboratory Branch at the CDC. It contains the genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species.
+This docker image contains the Reference Genome Database version 2 (RGDv2) from the Enteric Diseases Laboratory Branch at the CDC. It contains the genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species. Here is the publication describing the database: [https://doi.org/10.3389/fmicb.2023.1225207](https://doi.org/10.3389/fmicb.2023.1225207)
 
 The FASTA files for RGDv2 can be found within `/RGDv2/` inside the docker image.
 

fastani/1.34-RGDV2/README.md

@@ -6,7 +6,7 @@ Full documentation: https://github.com/ParBLiSS/FastANI
 
 FastANI was developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes.
 
-This docker image contains the Reference Genome Database version 2 (RGDv2) from the Enteric Diseases Laboratory Branch at the CDC. It contains the genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species.
+This docker image contains the Reference Genome Database version 2 (RGDv2) from the Enteric Diseases Laboratory Branch at the CDC. It contains the genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species. Here is the publication describing the database: [https://doi.org/10.3389/fmicb.2023.1225207](https://doi.org/10.3389/fmicb.2023.1225207)
 
 The FASTA files for RGDv2 can be found within `/RGDv2/` inside the docker image.
 

mummer/4.0.0-RGDv2/README.md

@@ -1,13 +1,15 @@
 # mummer + RGDv2 container
+
 Main tool : [mummer](https://github.com/mummer4/mummer)
 
 Additional tools:
+
 - `mash` v2.3
 - `ani-m.pl` v0.1 from https://github.com/lskatz/ani-m
 
 MUMmer is a versatile alignment tool for DNA and protein sequences.
 
-This docker image contains the **Reference Genome Database version 2 (RGDv2)** from the Enteric Diseases Laboratory Branch at the CDC. It contains the reference genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species.
+This docker image contains the **Reference Genome Database version 2 (RGDv2)** from the Enteric Diseases Laboratory Branch at the CDC. It contains the reference genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species. Here is the publication describing the database: [https://doi.org/10.3389/fmicb.2023.1225207](https://doi.org/10.3389/fmicb.2023.1225207)
 
 The FASTA files for RGDv2 can be found within the directory `/RGDv2/` inside the docker image.
 

mummer/4.0.0-gnuplot/README.md

@@ -11,7 +11,7 @@ Additional tools:
 
 MUMmer is a versatile alignment tool for DNA and protein sequences.
 
-This docker image contains the **Reference Genome Database version 2 (RGDv2)** from the Enteric Diseases Laboratory Branch at the CDC. It contains the reference genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species.
+This docker image contains the **Reference Genome Database version 2 (RGDv2)** from the Enteric Diseases Laboratory Branch at the CDC. It contains the reference genomes of 43 enteric bacterial isolates that are used to for species identification of bacterial isolate WGS data. This database is NOT meant to be comprehensive - it contains the genomes of enteric pathogens commonly sequenced by EDLB and some closely related species. Here is the publication describing the database: [https://doi.org/10.3389/fmicb.2023.1225207](https://doi.org/10.3389/fmicb.2023.1225207)
 
 The FASTA files for RGDv2 can be found within the directory `/RGDv2/` inside the docker image.
 

vadr/1.6.3-hav-flu2/README.md

@@ -22,6 +22,7 @@ Available VADR models:
 - Dengue virus and other Flaviviridae
 - RSV v1.5.1-2
 - influenza v1.6.3-2
+  - More information on this model can be found in the publication describing the creation, testing, and validation here: [https://doi.org/10.1093/database/baae091](https://doi.org/10.1093/database/baae091)
 
 Additional VADR models: