Galaxyの公共サーバ（微生物解析用）

[Galaxyの公共サーバ](https://qiita.com/haruosuz/items/f5c2e5c4212246e80d60)のうち、微生物（細菌/バクテリア、ウイルス）の解析に利用できるサーバを紹介します。

## [A-Game](https://galaxyproject.org/use/a-game/)
メタゲノム解析

- Public server: [A-Game server]()
- マニュアル [A-Game Manual](http://159.149.160.68/galaxy/static/manual/)

## [ARGs-OAP](https://galaxyproject.org/use/args-oap/)
メタゲノムにおける抗生物質耐性遺伝子の同定

- Public server: [ARGs-OAP Galaxy Server](https://smile.hku.hk/SARGs)
- マニュアル [manual page for ARGs-OAP](https://github.com/biofuture/Ublastx_stageone)
- 論文
  - [Yin et al. Bioinformatics. 2018 "ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes"](https://www.ncbi.nlm.nih.gov/pubmed/29408954)
  - [Yang et al. Bioinformatics. 2016 "ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database"](https://www.ncbi.nlm.nih.gov/pubmed/27153579)

## [BioMaS](https://galaxyproject.org/use/biomas/)
環境微生物群集の分類

- Public server: [BioMaS Galaxy](http://galaxy.cloud.ba.infn.it:8080/) This site can’t be reached
- 論文 [Fosso et al. BMC Bioinformatics. 2015 "BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS."](https://www.ncbi.nlm.nih.gov/pubmed/26130132)

## [BitLAB](https://galaxyproject.org/use/bitlab/)
メタゲノム解析

- Public server: [BitLAB Galaxy](https://pistacho.ac.uma.es/galaxy/root/login?redirect=%2Fgalaxy%2F)
- チュートリアル [extensive tutorial](http://www.bitlab-es.com/gecko/documents/GalaxyGuidedExercise.pdf) This site can’t be reached
- 論文 [Pérez-Wohlfeil et al. BMC Genomics. 2016 "Computational workflow for the fine-grained analysis of metagenomic samples."](https://www.ncbi.nlm.nih.gov/pubmed/27801291)

## [Center for Phage Technology (CPT)](https://galaxyproject.org/use/center-for-phage-technology-cpt/)
genbank/gff3形式ファイル処理ツール、ファージの自動アノテーション

- Public server: [Center for Phage Technology (CPT) Galaxy Server](https://cpt.tamu.edu/galaxy-pub/)

![](https://galaxyproject.org/use/center-for-phage-technology-cpt/cpt-logo.png)

## [Codon Harmonizer](https://galaxyproject.org/public-galaxy-servers/codon-harmonizer/)
大腸菌で異種遺伝子発現のためのコドン改変

- Public server: [Galaxy Server](http://codonharmonizer.systemsbiology.nl/)
- 論文 [Claassens NJ et al. PLoS One. 2017 "Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms."](https://www.ncbi.nlm.nih.gov/pubmed/28902855)

## [Huttenhower Lab](https://galaxyproject.org/use/huttenhower-lab/)
メタゲノム・機能的ゲノム解析

- pitagora日本語チュートリアル [Huttenhower_Lab_Workflows](http://wiki.pitagora-galaxy.org/wiki/index.php/Huttenhower_Lab_Workflows)

## [MBAC Metabiome Portal](https://galaxyproject.org/use/mbac-metabiome-portal/)
マイクロバイオーム、メタボローム、immunomeデータ（Metabiome）解析

- Public server: [MBAC Metabiome Server](http://mbac.gmu.edu:8080/)

## [MISSISSIPPI](https://galaxyproject.org/use/mississippi/)
エピジェネティクス、メタゲノミクス、RNA配列データ解析

- Public server: [MISSISSIPPI Server](https://mississippi.snv.jussieu.fr/)

## [Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB)](https://galaxyproject.org/use/mpdstb/)
疾患特有ウェブポータル。結核に対する創薬

- Public server: [Molecular Property Diagnostic Suite - Tuberculosis (MPDSTB)](http://mpds.osdd.net/)
- マニュアル [MPDSTB Manual](http://mpds.osdd.net/galaxy/static/view/Manual.pdf)
- 論文 
  - [Nagamani et al. SAR QSAR Environ Res. 2017 "Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery."](https://www.ncbi.nlm.nih.gov/pubmed/29206500)
  - [Gaur et al. J. Chem. Sci. 2017 "Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB)."](https://link.springer.com/article/10.1007%2Fs12039-017-1268-4)

## [Orione](https://galaxyproject.org/use/orione/)
微生物NGS解析。リードの前処理、マッピング、アセンブル、アノテーション、RNA-Seq、メタゲノム解析

- Public server: [Orione](https://orione.crs4.it/)
- 論文 [Cuccuru et al. Bioinformatics. 2014 "Orione, a web-based framework for NGS analysis in microbiology."](https://www.ncbi.nlm.nih.gov/pubmed/24618473)
- pitagora日本語チュートリアル [Orione-live-supplement](http://wiki.pitagora-galaxy.org/wiki/index.php/Orione-live-supplement)
- [Galaxy Teaching Hub](https://galaxyproject.org/teach/) [Microbial analysis with Orione](https://galaxyproject.org/teach/resource/microbial-with-orione/)

## [RNA-Rocket @ Pathogen Portal](https://galaxyproject.org/use/rna-rocket-pathogen-portal/)
感染症研究のためのRNA-Seq解析リソース。

- Public server: [RNA-Rocket at Pathogen Portal](http://rnaseq.pathogenportal.org/)
- 論文 [Warren et al. Bioinformatics. 2015 "RNA-Rocket: an RNA-Seq analysis resource for infectious disease research."](https://www.ncbi.nlm.nih.gov/pubmed/25573919)

## [USMI Galaxy Demonstrator](https://galaxyproject.org/public-galaxy-servers/usmi-galaxy-demonstrator/)
微生物の情報を統合。

- Public server: [USMI Galaxy Demonstrator](http://bioinformatics.hsanmartino.it:8080/)
- 査読なし論文 [NOT PEER-REVIEWED "USMI Galaxy Demonstrator (UGD): a collection of tools to integrate microorganisms information [PeerJ Preprints]"](https://peerj.com/preprints/2766/)

## [VarCap](https://galaxyproject.org/use/varcap/)
原核生物の変異（SNP, InDel, 構造多型）予測。

- Public server: [VarCap Galaxy](http://galaxy.csb.univie.ac.at:8080/) ログインが必要
- [Tutorial](http://galaxy.csb.univie.ac.at:8080/static/welcome.html)
- 論文 [Zojer M et al. PeerJ. 2017 "Variant profiling of evolving prokaryotic populations."](https://www.ncbi.nlm.nih.gov/pubmed/28224054)

## [VirAmp](https://galaxyproject.org/public-galaxy-servers/viramp/)
ウイルス ゲノム アセンブリ

- Public server: [VarCap Galaxy](http://galaxy.csb.univie.ac.at:8080/) ログインが必要
- 論文 [Wan et al. (2015) "VirAmp: a galaxy-based viral genome assembly pipeline."](https://www.ncbi.nlm.nih.gov/pubmed/25918639)
- pitagora日本語チュートリアル [VirAmp_Workflows](http://wiki.pitagora-galaxy.org/wiki/index.php/VirAmp_Workflows)