[{"_1":2,"_151":-5,"_152":-5},"loaderData",{"_3":4,"_17":18,"_24":25,"_144":145},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":11,"_23":21},"username","isAskGordonEnabled",true,"showMinimalLanding","showHoneypotTrap","routes/_layout.layers.$namespace.$reponame.$tag.(images).($imageUrlDigest)",{"_26":27,"_28":29,"_70":71,"_72":-7,"_73":-7,"_74":-7,"_75":-7,"_76":-5,"_77":-5,"_78":11,"_79":11,"_64":80,"_134":21,"_105":61,"_135":104,"_136":63,"_41":42,"_137":11,"_138":21,"_139":44,"_140":-5,"_141":11,"_142":11,"_143":11},"scanningType","none","tagData",{"_30":31,"_32":33,"_34":35,"_36":37,"_57":58,"_59":31,"_60":61,"_62":63,"_64":65,"_66":46,"_67":58,"_68":55,"_69":21},"creator",3229322,"full_size",434149569,"id",67640999,"images",[38],{"_39":40,"_41":42,"_43":44,"_45":46,"_47":48,"_49":50,"_51":44,"_52":-5,"_53":33,"_54":55,"_56":-5},"architecture","amd64","digest","sha256:de293f51b0e8159cfb79d2bf19d97daea541d02919c7dd2364e80696318a18a2","features","","last_pulled","2026-11-11T17:08:57.837765422Z","last_pushed","2019-09-03T14:15:07Z","os","linux","os_features","os_version","size","status","active","variant","last_updated","2019-09-03T18:06:07.892291Z","last_updater","last_updater_username","staphb","name","latest","repository",7643916,"tag_last_pulled","tag_last_pushed","tag_status","v2","tagImages",[],"layerOrdinals","packageName","cveId","sbom","scoutSummary","staticSummary","isScoutPaymentRequired","canSeeVulnerabilities",{"_81":82,"_90":91,"_93":94,"_95":96,"_97":11,"_57":98,"_99":100,"_101":102,"_62":104,"_105":61,"_106":107,"_108":92,"_109":110,"_54":111,"_112":55,"_113":-5,"_114":110,"_115":116,"_117":11,"_118":61,"_119":120,"_125":11,"_126":127,"_131":61,"_132":133},"categories",[83,87],{"_62":84,"_85":86},"Machine learning & AI","slug","machine-learning-and-ai",{"_62":88,"_85":89},"Data science","data-science","content_types",[92],"image","date_registered","2019-09-03T13:46:52.06334Z","description","Assign emm type and subtype by querying the CDC M-type specific database for Group A Strep","is_private","2019-09-04T14:34:08.304458Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[103],"application/vnd.docker.container.image.v1+json","emm-typing-tool","namespace","pull_count",72274,"repository_type","star_count",0,1,"status_description","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 * [@k-florek](https://github.com/k-florek)\n * [@garfinjm](https://github.com/garfinjm)\n * [@kevinlibuit](https://github.com/kevinlibuit)\n * [@Ikkik](https://github.com/Ikkik)\n * [@lskatz](https://github.com/lskatz)\n * [@stjacqrm](https://github.com/stjacqrm)\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://chstno1.isgood.host/r/staphb/)\n[![Build Status](https://travis-ci.com/StaPH-B/docker-builds.svg?branch=master)](https://travis-ci.com/StaPH-B/docker-builds) (Build only reflects those containers that have been added to the TravisCI tests)\n\n| Software | Version | Link |\n| :--------: | :-------: | -------- |\n| [ABRicate](https://chstno1.isgood.host/r/staphb/abricate/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/abricate.svg?style=popout)](https://chstno1.isgood.host/r/staphb/abricate) | 0.8.7, 0.8.13, 0.8.13s (+serotypefinder db) | https://github.com/tseemann/abricate |\n| [BWA](https://chstno1.isgood.host/r/staphb/bwa)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/bwa.svg?style=popout)](https://chstno1.isgood.host/r/staphb/bwa) | 0.7.17 | https://github.com/lh3/bwa |\n| [Canu-Racon](https://chstno1.isgood.host/r/staphb/canu-racon/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/canu-racon.svg?style=popout)](https://chstno1.isgood.host/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| [CDC-SPN](https://chstno1.isgood.host/r/staphb/cdc-spn/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cdc-spn.svg?style=popout)](https://chstno1.isgood.host/r/staphb/cdc-spn) | 0.1 (no version) | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |\n| [cfsan-snp-pipeline](https://chstno1.isgood.host/r/staphb/cfsan-snp-pipeline)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cfsan-snp-pipeline.svg?style=popout)](https://chstno1.isgood.host/r/staphb/cfsan-snp-pipeline) | 2.0.2 | https://github.com/CFSAN-Biostatistics/snp-pipeline |\n| [emm-typing-tool](https://chstno1.isgood.host/r/staphb/emm-typing-tool)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/emm-typing-tool.svg?style=popout)](https://chstno1.isgood.host/r/staphb/emm-typing-tool) | 0.0.1 (no version) | https://github.com/phe-bioinformatics/emm-typing-tool |\n| [FastANI](https://chstno1.isgood.host/r/staphb/fastani)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/fastani.svg?style=popout)](https://chstno1.isgood.host/r/staphb/fastani) | 1.1 | https://github.com/ParBLiSS/FastANI |\n| [Filtlong](https://chstno1.isgood.host/r/staphb/filtlong)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/filtlong.svg?style=popout)](https://chstno1.isgood.host/r/staphb/filtlong) | 0.2.0 | https://github.com/rrwick/filtlong |\n| [Flye](https://chstno1.isgood.host/r/staphb/flye)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/flye.svg?style=popout)](https://chstno1.isgood.host/r/staphb/flye) | 2.5 | https://github.com/fenderglass/Flye |\n| [iqtree](https://chstno1.isgood.host/r/staphb/iqtree/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/iqtree.svg?style=popout)](https://chstno1.isgood.host/r/staphb/iqtree) | 1.6.7 | http://www.iqtree.org/ |\n| [Kraken](https://chstno1.isgood.host/r/staphb/kraken/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/kraken.svg?style=popout)](https://chstno1.isgood.host/r/staphb/kraken) | 1.0, 1.1.1 | https://github.com/DerrickWood/kraken |\n| [kSNP3](https://chstno1.isgood.host/r/staphb/ksnp3/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/ksnp3.svg?style=popout)](https://chstno1.isgood.host/r/staphb/ksnp3)| 3.1 | https://sourceforge.net/projects/ksnp/ |\n| [Lyve-SET (includes CG-Pipeline scripts and raxml)](https://chstno1.isgood.host/r/staphb/lyveset/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/lyveset.svg?style=popout)](https://chstno1.isgood.host/r/staphb/lyveset) | 1.1.4f, 2.0.1 (lyve-SET) | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |\n| [Mash](https://chstno1.isgood.host/r/staphb/mash/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mash.svg?style=popout)](https://chstno1.isgood.host/r/staphb/mash) | 2.1 | https://github.com/marbl/Mash |\n| [mashtree](https://chstno1.isgood.host/r/staphb/mashtree)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mashtree.svg?style=popout)](https://chstno1.isgood.host/r/staphb/mashtree) | 0.52.0 | https://github.com/lskatz/mashtree |\n| [medaka](https://chstno1.isgood.host/r/staphb/medaka)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/medaka.svg?style=popout)](https://chstno1.isgood.host/r/staphb/medaka) | 0.8.1 | https://github.com/nanoporetech/medaka |\n| [mlst](https://chstno1.isgood.host/r/staphb/mlst)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mlst.svg?style=popout)](https://chstno1.isgood.host/r/staphb/mlst) | 2.16.2 | https://github.com/tseemann/mlst |\n| [Prokka](https://chstno1.isgood.host/r/staphb/prokka/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/prokka.svg?style=popout)](https://chstno1.isgood.host/r/staphb/prokka) | 1.13.4, 1.14.0 | https://github.com/tseemann/prokka |\n| [QUAST](https://chstno1.isgood.host/r/staphb/quast/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/quast.svg?style=popout)](https://chstno1.isgood.host/r/staphb/quast) | 5.0.0, 5.0.2 | https://github.com/ablab/quast |\n| [Roary](https://chstno1.isgood.host/r/staphb/roary/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/roary.svg?style=popout)](https://chstno1.isgood.host/r/staphb/roary) | 3.12.0 | https://github.com/sanger-pathogens/Roary |\n| [SalmID](https://chstno1.isgood.host/r/staphb/salmid)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/salmid.svg?style=popout)](https://chstno1.isgood.host/r/staphb/salmid) | 0.1.23 | https://github.com/hcdenbakker/SalmID |\n| [Samtools](https://chstno1.isgood.host/r/staphb/samtools)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/samtools.svg?style=popout)](https://chstno1.isgood.host/r/staphb/samtools) | 1.9 | https://github.com/samtools/samtools |\n| [SeqSero](https://chstno1.isgood.host/r/staphb/seqsero/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero.svg?style=popout)](https://chstno1.isgood.host/r/staphb/seqsero) | 1.0.1 | https://github.com/denglab/SeqSero |\n| [SeqSero2](https://chstno1.isgood.host/r/staphb/seqsero2/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero2.svg?style=popout)](https://chstno1.isgood.host/r/staphb/seqsero2) | 0.1.0, 1.0.0 | https://github.com/denglab/SeqSero2/ |\n| [seqyclean](https://chstno1.isgood.host/r/staphb/seqyclean)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqyclean.svg?style=popout)](https://chstno1.isgood.host/r/staphb/seqyclean) | 1.10.09 | https://github.com/ibest/seqyclean |\n| [SerotypeFinder](https://chstno1.isgood.host/r/staphb/serotypefinder/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/serotypefinder.svg?style=popout)](https://chstno1.isgood.host/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| [Shovill](https://chstno1.isgood.host/r/staphb/shovill/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/shovill.svg?style=popout)](https://chstno1.isgood.host/r/staphb/shovill) | 1.0.4 | https://github.com/tseemann/shovill |\n| [SISTR](https://chstno1.isgood.host/r/staphb/sistr/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sistr.svg?style=popout)](https://chstno1.isgood.host/r/staphb/sistr) | 1.0.2 | https://github.com/peterk87/sistr_cmd |\n| [SKESA](https://chstno1.isgood.host/r/staphb/skesa)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/skesa.svg?style=popout)](https://chstno1.isgood.host/r/staphb/skesa) | 2.3.0 | https://github.com/ncbi/SKESA |\n| [snp-dists](https://chstno1.isgood.host/r/staphb/snp-dists)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/snp-dists.svg?style=popout)](https://chstno1.isgood.host/r/staphb/snp-dists) | 0.6.2 | https://github.com/tseemann/snp-dists |\n| [SPAdes](https://chstno1.isgood.host/r/staphb/spades/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/spades.svg?style=popout)](https://chstno1.isgood.host/r/staphb/spades) | 3.12.0, 3.13.0 | http://cab.spbu.ru/software/spades/ |\n| [SRA-toolkit](https://chstno1.isgood.host/r/staphb/sratoolkit/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sratoolkit.svg?style=popout)](https://chstno1.isgood.host/r/staphb/sratoolkit) | 2.9.2 | https://github.com/ncbi/sra-tools |\n| [Staramr](https://chstno1.isgood.host/r/staphb/staramr/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/staramr.svg?style=popout)](https://chstno1.isgood.host/r/staphb/staramr) | 0.5.1 | https://github.com/phac-nml/staramr |\n| [Trimmomatic](https://chstno1.isgood.host/r/staphb/trimmomatic/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/trimmomatic.svg?style=popout)](https://chstno1.isgood.host/r/staphb/trimmomatic) | 0.38, 0.39 | http://www.usadellab.org/cms/?page=trimmomatic |\n| [Unicycler](https://chstno1.isgood.host/r/staphb/unicycler/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/unicycler.svg?style=popout)](https://chstno1.isgood.host/r/staphb/unicycler) | 0.4.7 | https://github.com/rrwick/Unicycler |\n\nYou can also view the list of images on Docker hub here: https://chstno1.isgood.host/r/staphb/\n","has_starred","hub_user","immutable_tags_settings",{"_121":11,"_122":123},"enabled","rules",[124],".*","is_automated","permissions",{"_128":21,"_129":11,"_130":11},"read","write","admin","user","storage_size",1160339784,"isOrg","reponame","tag","canDeleteTags","isHubSbxKitsEnabled","currentTab","tagAttestations","displaySecurityMetadata","showSbxLogoOverride","showSbxAgenticPlatformBadge","routes/_layout.layers.$namespace.$reponame.$tag.(images).($imageUrlDigest)._index",{"_26":27,"_74":-7,"_72":-7,"_73":-7,"_28":146,"_41":42,"_149":-7,"_150":11},{"_30":31,"_32":33,"_34":35,"_36":147,"_57":58,"_59":31,"_60":61,"_62":63,"_64":65,"_66":46,"_67":58,"_68":55,"_69":21},[148],{"_39":40,"_41":42,"_43":44,"_45":46,"_47":48,"_49":50,"_51":44,"_52":-5,"_53":33,"_54":55,"_56":-5},"imageWithLayers","hasPermissionToViewRepoSettings","actionData","errors"]

staphb/emm-typing-tool:latest