From 617039fa8373ccd640ae130ec8d85ad214b03e5c Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Sat, 9 Nov 2024 17:49:42 +0000 Subject: [PATCH 1/3] add reference to publication describing VADR influenza model creation/testing/validation --- vadr/1.6.3-hav-flu2/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/vadr/1.6.3-hav-flu2/README.md b/vadr/1.6.3-hav-flu2/README.md index 4509a072a..18bacf245 100644 --- a/vadr/1.6.3-hav-flu2/README.md +++ b/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: From a3c8a0adf10f1f5e26ec60b3b7eb7386bebb6d9a Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Sat, 9 Nov 2024 17:56:17 +0000 Subject: [PATCH 2/3] added links to publication describing RGDv2 in readmes for docker iamges that contain the db. closes #824 --- fastani/1.33-RGDv2/README.md | 2 +- fastani/1.34-RGDV2/README.md | 2 +- mummer/4.0.0-RGDv2/README.md | 4 +++- mummer/4.0.0-gnuplot/README.md | 2 +- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/fastani/1.33-RGDv2/README.md b/fastani/1.33-RGDv2/README.md index e27a4dbf0..9104ab75a 100644 --- a/fastani/1.33-RGDv2/README.md +++ b/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. diff --git a/fastani/1.34-RGDV2/README.md b/fastani/1.34-RGDV2/README.md index e27a4dbf0..9104ab75a 100644 --- a/fastani/1.34-RGDV2/README.md +++ b/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. diff --git a/mummer/4.0.0-RGDv2/README.md b/mummer/4.0.0-RGDv2/README.md index ff1c03786..9c09e8a3d 100755 --- a/mummer/4.0.0-RGDv2/README.md +++ b/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. diff --git a/mummer/4.0.0-gnuplot/README.md b/mummer/4.0.0-gnuplot/README.md index 5e5cbab34..58af5c89c 100755 --- a/mummer/4.0.0-gnuplot/README.md +++ b/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. From b1f4a42a7850f7dee5d9f2d480ee2bf22c32295f Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Sun, 10 Nov 2024 10:37:04 -0500 Subject: [PATCH 3/3] Update README.md fix markdown bullet --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 23aa8b187..3186a0d1e 100644 --- a/README.md +++ b/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)
[![docker pulls](https://badgen.net/docker/pulls/staphb/medaka)](https://hub.docker.com/r/staphb/medaka) |
  • [0.8.1](./medaka/0.8.1/)
  • [1.0.1](./medaka/1.0.1/)
  • [1.2.0](./medaka/1.2.0/)
  • [2.0.0](./medaka/2.0.0/)
  • [2.0.1](./medaka/2.0.1/)
| https://github.com/nanoporetech/medaka | | [metaphlan](https://hub.docker.com/r/staphb/metaphlan)
[![docker pulls](https://badgen.net/docker/pulls/staphb/metaphlan)](https://hub.docker.com/r/staphb/metaphlan) |
  • [3.0.3-no-db (no database)](./metaphlan/3.0.3-no-db/)
  • [3.0.3 (~3GB db)](./metaphlan/3.0.3/)
  • [4.1.0](./metaphlan/4.1.0/) (no database)
  • [4.1.1](./metaphlan/4.1.1/) (no database)
| https://github.com/biobakery/MetaPhlAn | | [MIDAS](https://hub.docker.com/r/staphb/midas)
[![docker pulls](https://badgen.net/docker/pulls/staphb/midas)](https://hub.docker.com/r/staphb/midas) |
  • 1.3.2 (no database)
  • | https://github.com/snayfach/MIDAS | -| [minimap2](https://hub.docker.com/r/staphb/minimap2)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) |
    • 2.17
    • 2.18
    • 2.21
    • 2.22
    • 2.23
    • 2.24
    • 2.25
    • [2.26](./minimap2/2.26)
    • [2.27](./minimap2/2.27/)
    • li>[2.28](./minimap2/2.28/)
    | https://github.com/lh3/minimap2 | +| [minimap2](https://hub.docker.com/r/staphb/minimap2)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/minimap2)](https://hub.docker.com/r/staphb/minimap2) |
    • 2.17
    • 2.18
    • 2.21
    • 2.22
    • 2.23
    • 2.24
    • 2.25
    • [2.26](./minimap2/2.26)
    • [2.27](./minimap2/2.27/)
    • [2.28](./minimap2/2.28/)
    | https://github.com/lh3/minimap2 | | [minipolish](https://hub.docker.com/r/staphb/minipolish)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/minipolish)](https://hub.docker.com/r/staphb/minipolish) |
    • 0.1.3
    | https://github.com/rrwick/Minipolish | | [mlst](https://hub.docker.com/r/staphb/mlst)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/mlst)](https://hub.docker.com/r/staphb/mlst) |
    • 2.16.2
    • 2.17.6
    • 2.19.0
    • 2.22.0
    • 2.22.1
    • 2.23.0
    • [2.23.0-2023-07 (databases updated July 2023)](mlst/2.23.0-2023-07/)
    • [2.23.0-2023-08 (databases updated Aug 2023)](mlst/2.23.0-2023-08/)
    • [2.23.0-2024-01 (databases updated Jan 2024)](mlst/2.23.0-2024-01/)
    • [2.23.0-2024-03 (databases updated March 2024)](mlst/2.23.0-2024-03/)
    | https://github.com/tseemann/mlst | | [Mugsy](https://hub.docker.com/r/staphb/mugsy)
    [![docker pulls](https://badgen.net/docker/pulls/staphb/mugsy)](https://hub.docker.com/r/staphb/mugsy) |
    • 1r2.3
    | http://mugsy.sourceforge.net/ |