The following data is compiled from a questionnaire of Q4 2022 and is targeted at groups funded under NFDI4Microbiota, that have a particular application/pipeline/database (henceforth referred to just as “tool”) already implemented or in inception that should be integrated and endorsed by the NFDI4Microbiota umbrella.
The goal is to gather this information centrally in NFDI4Microbiota to assess the span of tools and derive consortium-wide guidelines for the tightest integration possible.
Disclaimer: Changes in the tool display
We recently created a NFDI4Microbiota domain on the life sciences software registry bio.tools and we will soon be displaying all the tools that NFDI4Microbiota created as well as the ones that NFDI4Microbiota consortium members endorse and highly recommend.
Thank you for your patience while we sort out editing rights and collection labels.
In the meantime, browse our tools below and find more recommendations for resources on reproducible data analysis.
Applications
checkM2 (EMBL)
Assessing the quality of metagenome-derived genome bins using machine learning
operating system: Linux
License: GPL 3.0
Link: https://github.com/chklovski/CheckM2
Eggnog mapper (EMBL)
Fast genome-wide functional annotation through orthology assignment
operating system: Linux, MacOS, Windows
License: AGPL 3.0
Link: https://github.com/eggnogdb/eggnog-mapper
GUNC (EMBL)
Python package for detection of chimerism and contamination in prokaryotic genomes.
operating system: Linux, MacOS, Windows
License: GPL 3.0
Link: https://github.com/grp-bork/gunc
mOTUs (EMBL)
A computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.
operating system: Linux
License: GPL 3.0
Link: https://github.com/motu-tool/mOTUs
Proteinortho (UMR)
Proteinortho is a tool to detect orthologous genes within different species.
operating system: Linux, MacOS
License: LGPL 3.0
Link: https://gitlab.com/paulklemm_PHD/proteinortho
Benchmarks
AMBER (Helmholtz-HZI)
Assessment of Metagenome BinnERs
operating system: Linux
License: GPL 3.0
Link: https://github.com/CAMI-challenge/AMBER
Databases
BacDive (DSMZ)
“BacDive is the worldwide largest database for standardized bacterial information.
operating system: Linux
License: CC BY
Link: https://bacdive.dsmz.de/
EggNOG Database (EMBL)
“A database of orthology relationships, functional annotation,
operating system: Linux
License: unknown
Link: http://eggnog5.embl.de/#/app/home
MediaDive (DSMZ)
Standardized cultivation media database
operating system: Linux, MacOS, Windows
License: CC BY
Link: https://mediadive.dsmz.de
HumanMetagenomeDB (UFZ)
“Explore and download curated human metagenome metadata. HumanMetagenomeDB (version 1.0) contains metadata of 69,822 metagenome samples.
operating system: Platform independent
License: CC BY
Link: https://web.app.ufz.de/hmgdb/
MarineMetagenomeDB (UFZ)
“Explore and download curated marine metagenome metadata. MarineMetagenomeDB (Release 1.0) contains standardized metadata of 11,449 marine metagenome samples.
operating system: Platform independent
License: GPL 3.0
Link: https://web.app.ufz.de/marmdb/
AnimalAssociatedMetagenomeDB (UFZ)
“Explore and download curated animal-associated metagnome metadata. The AnimalAssociatedMetagenomeDB (version 1.0) contains 10,885 metagenome samples.
operating system: Platform independent
License: GPL 3.0
Link: https://webapp.ufz.de/aamdb/
TerrestrialMetagenomeDB (UFZ)
“Explore and download curated terrestrial metagenome metadata. TerrestrialMetagenomeDB (release 1.0) includes 15,022 terrestrial metagenome samples.
operating system: Platform independent
License: CC BY
Link: https://webapp.ufz.de/tmdb
Pipelines
BioAutoML (UFZ)
BioAutoML: Automated Feature Engineering and Metalearning for Classification of Biological Sequences
operating system: Linux, MacOS
License: BSD3
Link: https://github.com/Bonidia/BioAutoML
CAMISIM (Helmholtz-HZI)
Model abundance distributions of microbial communities and simulate metagenome datasets
operating system: Linux
License: Apache 2
Link: https://github.com/CAMI-challenge/CAMISIM
MetaProteomeAnalyzer (ISAS)
Workflow for metaproteomics anaylysis of microbiomes
operating system: Linux, Windows
License: Apache 2
Link: https://github.com/compomics/meta-proteome-analyzer
Multi-Domain Genome Recovery (MuDoGeR) (UFZ)
The Multi-Domain Genome Recovery v1.0.1 (MuDoGeR v1.0.1) framework is a tool developed to help recover Metagenome-Assembled Genomes (MAGs) - from prokaryotes and eukaryotes - and Uncultivated Viral Genomes (UViGs) from whole-genome sequence (WGS) samples simultaneously.
The MuDoGeR v1.0.1 framework act as a wrapper of several tools. Available as a singularity container of via conda installation.
It was designed to be an easy-to-use tool that outputs ready-to-use comprehensive files.
operating system: Linux
License: GPL 3.0
Link: https://github.com/mdsufz/MuDoGeR
OrtSuite (UFZ)
Flexible pipeline for annotation of ecosystem processes and prediction of putative microbial interactions
operating system: Linux
License: CC BY
Link: https://github.com/mdsufz/OrtSuite
PredicTF (UFZ)
Tool to predict bacterial transcription factors in complex microbial communities
operating system: Linux
License: CC BY
Link: https://github.com/mdsufz/PredicTF
Protologger (UKAachen)
Protologger is a bioinformatic tool that automatically generates all the necessary readouts for writing a detailed protologue.
By producing multiple taxonomic outputs, functional features and ecological analysis using the 16S rRNA gene and genome sequences from a single species, the time needed to gather the information for describing novel taxa is substantially reduced.
operating system: Linux
License: CC BY
Link: http://protologger.de/
Qiita (JLU)
Best practice microbiome analysis suite
operating system: Linux
License: BSD3
Link: https://qiita.ucsd.edu/
Webservices
iPath (EMBL)
Interactive Pathways Explorer (iPath) is a web-based tool for the visualization, analysis and customization of various pathway maps.
operating system: Linux
License: GPL
Link: https://pathways.embl.de/
iTOL (EMBL)
Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic and other trees.
operating system: Linux
License: paid
Link: https://itol.embl.de/
Help Desk (ZBMED)
Utility flask app for contact notification on the NFDI4Microbiota homepage
operating system: Linux
License: NA
Link: https://nfdi4microbiota.de/contact-form/