Available Tools of NFDI4Microbiota members
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.
Applications
checkM2 (EMBL)
Assessing the quality of metagenome-derived genome bins using machine learning
operating system: Linux
license: GNU
link: https://github.com/chklovski/CheckM2
Eggnog mapper (EMBL)
Fast genome-wide functional annotation through orthology assignment
operating system: Linux, MacOS, Windows
license: GNU
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: GNU
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: GNU
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: GNU
link: https://gitlab.com/paulklemm_PHD/proteinortho
Benchmarks
AMBER (Helmholtz-HZI)
Assessment of Metagenome BinnERs
operating system: Linux
license: GPL
link: https://github.com/CAMI-challenge/AMBER
Databases
BacDive (DSMZ)
“BacDive is the worldwide largest database for standardized bacterial information.
operating system: Linux
license: GNU
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://eggnog5.embl.dend
MediaDive (DSMZ)
Standardized cultivation media database
operating system: Linux, MacOS, Windows
license: CC4
link: https://mediadive.dsmz.de
Pipelines
BioAutoML (UFZ)
BioAutoML: Automated Feature Engineering and Metalearning for Classification of Biological Sequences
operating system: Linux, MacOS
license: NA
link: https://github.com/Bonidia/BioAutoML
CAMISIM (Helmholtz-HZI)
Model abundance distributions of microbial communities and simulate metagenome datasets
operating system: Linux
license: Apache
link: https://github.com/CAMI-challenge/CAMISIM
MetaProteomeAnalyzer (ISAS)
Workflow for metaproteomics anaylysis of microbiomes
operating system: Linux, Windows
license: Apache
link: https://github.com/compomics/meta-proteome-analyzer
MuDoGeR (UFZ)
The Multi-Domain Genome Recovery v1.0 (MuDoGeR v1.0) 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 framework act as a wrapper of several tools.
It was designed to be an easy-to-use tool that outputs ready-to-use comprehensive files.
operating system: Linux
license: GNU
link: https://github.com/mdsufz/MuDoGeR
Multi-Domain Genome Recovery (MuDoGeR) (UFZ)
Recover eukaryotic, prokaryotic, and viral metagenome-assembled genomes from a single metagenomic sample
operating system: Linux
license: GNU
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: CC4
link: https://github.com/mdsufz/OrtSuite,
PredicTF (UFZ)
Tool to predict bacterial transcription factors in complex microbial communities
operating system: Linux
license: CC4
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: unsure
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/
None (ZBMED)
Utility flask app for contact notification on the NFDI4Microbiota homepage
operating system: Linux
license: NA