[{"_1":2,"_228":-5,"_229":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_196":197},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":17},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_92":93,"_117":118,"_187":-5,"_188":11,"_189":17,"_190":11,"_191":-5,"_192":11,"_193":-5,"_194":195},"canonicalUrl","https://hub.docker.com/r/staphb/cdc-spn/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","staphb","reponame","cdc-spn","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_46":47,"_49":50,"_51":52,"_53":11,"_54":55,"_56":57,"_58":59,"_39":31,"_28":29,"_62":63,"_64":48,"_65":66,"_67":68,"_69":70,"_71":-5,"_72":66,"_73":74,"_75":11,"_76":29,"_77":78,"_83":11,"_84":85,"_89":29,"_90":91},"categories",[38,43],{"_39":40,"_41":42},"name","Machine learning & AI","slug","machine-learning-and-ai",{"_39":44,"_41":45},"Data science","data-science","content_types",[48],"image","date_registered","2019-02-04T02:25:41.167602Z","description","Scripts and reference files to type streptococcus pneumoniae","is_private","last_updated","2026-05-19T21:31:47.182442Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[60,61],"application/vnd.docker.container.image.v1+json","application/vnd.oci.image.index.v1+json","pull_count",21716,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# [docker-builds](#)\nThis repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of programs used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.\n\nEach Dockerfile lists author/maintainer for that specific Docker image, but the authors/maintainers of the docker images are:\n * [@kapsakcj](https://github.com/kapsakcj)\n * [@nwflorek](https://github.com/nwflorek)\n * [@garfinjm](https://github.com/garfinjm)\n\nIf you would like to contribute with your own Docker image or perhaps improve upon the existing images, please fork the repository, make your changes/additions, and submit a pull request. If you are having an issue with an existing image, please submit an issue. We welcome any and all feedback! \n[See more details on how to contribute here](https://staph-b.github.io/docker-builds/contribute/)\n\n## [Docker User Guide](https://staph-b.github.io/docker-builds/)\nWe have also created a user guide that outlines methods and best practices for using and developing docker containers. \n[Docker User Guide](https://staph-b.github.io/docker-builds/)\n\n## [Available Docker images](https://hub.docker.com/r/staphb/)\n| Software | Version | Link |\n| :--------: | :-------: | -------- |\n| [SRA-toolkit](https://hub.docker.com/r/staphb/sratoolkit/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sratoolkit.svg?style=popout)](https://hub.docker.com/r/staphb/sratoolkit) | 2.9.2 | https://github.com/ncbi/sra-tools |\n| [Lyve-SET (includes CG-Pipeline scripts and raxml)](https://hub.docker.com/r/staphb/lyveset/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/lyveset.svg?style=popout)](https://hub.docker.com/r/staphb/lyveset) | 1.1.4f, 2.0.1 (lyve-SET) | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |\n| [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/kraken.svg?style=popout)](https://hub.docker.com/r/staphb/kraken) | 1.0 | https://github.com/DerrickWood/kraken |\n| [SPAdes](https://hub.docker.com/r/staphb/spades/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/spades.svg?style=popout)](https://hub.docker.com/r/staphb/spades) | 3.12.0, 3.13.0 | http://cab.spbu.ru/software/spades/ |\n| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/quast.svg?style=popout)](https://hub.docker.com/r/staphb/quast) | 5.0.0 | https://github.com/ablab/quast |\n| [Mash](https://hub.docker.com/r/staphb/mash/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mash.svg?style=popout)](https://hub.docker.com/r/staphb/mash) | 2.1 | https://github.com/marbl/Mash |\n| [SerotypeFinder](https://hub.docker.com/r/staphb/serotypefinder/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/serotypefinder.svg?style=popout)](https://hub.docker.com/r/staphb/serotypefinder) | 1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image) | https://bitbucket.org/genomicepidemiology/serotypefinder/ |\n| [SeqSero](https://hub.docker.com/r/staphb/seqsero/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero.svg?style=popout)](https://hub.docker.com/r/staphb/seqsero) | 1.0.1 | https://github.com/denglab/SeqSero |\n| [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero2.svg?style=popout)](https://hub.docker.com/r/staphb/seqsero2) | 0.1.0 | https://github.com/denglab/SeqSero2/ |\n| [SISTR](https://hub.docker.com/r/staphb/sistr/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sistr.svg?style=popout)](https://hub.docker.com/r/staphb/sistr) | 1.0.2 | https://github.com/peterk87/sistr_cmd |\n| [ABRicate](https://hub.docker.com/r/staphb/abricate/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/abricate.svg?style=popout)](https://hub.docker.com/r/staphb/abricate) | 0.8.7 | https://github.com/tseemann/abricate |\n| [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/prokka.svg?style=popout)](https://hub.docker.com/r/staphb/prokka) | 1.13 | https://github.com/tseemann/prokka |\n| [Trimmomatic](https://hub.docker.com/r/staphb/trimmomatic/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/trimmomatic.svg?style=popout)](https://hub.docker.com/r/staphb/trimmomatic) | 0.38 | http://www.usadellab.org/cms/?page=trimmomatic |\n| [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/iqtree.svg?style=popout)](https://hub.docker.com/r/staphb/iqtree) | 1.6.7 | http://www.iqtree.org/ |\n| [Unicycler](https://hub.docker.com/r/staphb/unicycler/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/unicycler.svg?style=popout)](https://hub.docker.com/r/staphb/unicycler) | 0.4.7 | https://github.com/rrwick/Unicycler |\n| [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/canu-racon.svg?style=popout)](https://hub.docker.com/r/staphb/canu-racon) | 1.7.1 (Canu) 1.3.1 (Racon) 2.13 (minimap2) | https://canu.readthedocs.io/en/latest/ https://github.com/isovic/racon https://lh3.github.io/minimap2/ |\n|[Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/roary.svg?style=popout)](https://hub.docker.com/r/staphb/roary) | 3.12.0 | https://github.com/sanger-pathogens/Roary |\n|[CDC-SPN](https://hub.docker.com/r/staphb/cdc-spn/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cdc-spn.svg?style=popout)](https://hub.docker.com/r/staphb/cdc-spn) | 0.1 (no version) | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |\n| [Shovill](https://hub.docker.com/r/staphb/shovill/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/shovill.svg?style=popout)](https://hub.docker.com/r/staphb/shovill) | 1.0.4 | https://github.com/tseemann/shovill |\n| [BWA](https://hub.docker.com/r/staphb/bwa)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/bwa.svg?style=popout)](https://hub.docker.com/r/staphb/bwa) | 0.7.17 | https://github.com/lh3/bwa |\n| [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/samtools.svg?style=popout)](https://hub.docker.com/r/staphb/samtools) | 1.9 | https://github.com/samtools/samtools |\n| [cfsan-snp-pipeline](https://hub.docker.com/r/staphb/cfsan-snp-pipeline)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cfsan-snp-pipeline.svg?style=popout)](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) | 2.0.2 | https://github.com/CFSAN-Biostatistics/snp-pipeline |\n\nYou can also view the list of images on Docker hub here: https://hub.docker.com/r/staphb/\n","has_starred","hub_user","immutable_tags_settings",{"_79":11,"_80":81},"enabled","rules",[82],".*","is_automated","permissions",{"_86":17,"_87":11,"_88":11},"read","write","admin","user","storage_size",3106362365,"orgData",{"_94":95,"_96":97,"_98":99,"_100":29,"_101":102,"_103":104,"_105":106,"_107":108,"_109":110,"_111":112,"_113":104,"_114":115,"_116":17},"id","2879f6c1219644f08dac94f6ffde26a2","uuid","2879f6c1-2196-44f0-8dac-94f6ffde26a2","type","organization","orgname","full_name","StaPH-B","location","","company","State Public Health Bioinformatics 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staphb/cdc-spn

Tags for staphb/cdc-spn