Bioinformatics Tools and Resources

Virtual Metabolic Human

Publication:

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Resource Available:

https://vmh.life/

AGORA2: Assembly of Gut Organisms through Reconstruction and Analysis, version 2

Publication:

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Resource Available:

https://vmh.life/

APOLLO

Publication:

APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

Resource Available:

https://vmh.life/

COBRA Toolbox: COnstraint-Based Reconstruction and Analysis

Publication:

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Resource Available:

https://github.com/opencobra/cobratoolbox/

Whole‐body metabolic reconstructions

Publication:

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

Resource Available:

https://github.com/opencobra/

DEMETER: Data-drivEn METabolic nEtwork Refinement

Publication:

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Resource Available:

https://github.com/opencobra/

Microbiome Modelling Toolbox 2.0

Resource Available:

https://github.com/opencobra/microbiomeModelingToolbox

MetaboAnnotator

Publication:

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions

Resource Available:

https://github.com/opencobra/

Infant whole-body models

Publication:

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

Resource Available:

https://github.com/opencobra/

MARS: Microbial Abundances Retrieved from Sequencing data

Publication:

Microbial Abundances Retrieved from Sequencing data—automated NCBI Taxonomy (MARS): a pipeline to create relative microbial abundance data for the Microbiome Modelling Toolbox and utilizing homosynonyms for efficient mapping to resources

Resource Available:

https://github.com/ThieleLab/MARS

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Publication:

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Resource Available:

https://github.com/grp-bork/spire

GUNC: the Genome UNClutterer

Publication:

GUNC: detection of chimerism and contamination in prokaryotic genomes

Resource Available:

https://github.com/grp-bork/gunc

ANANSI: ANnotation-based ANalysis of Specific Interactions

Publication:

Knowledge-based Integration of Multi-Omic Datasets with Anansi: Annotation-based Analysis of Specific Interactions

Resource Available:

https://github.com/thomazbastiaanssen/anansi

KRONOS

Publication:

Kronos: A computational tool to facilitate biological rhythmicity analysis

Resource Available:

https://github.com/thomazbastiaanssen/kronos

Volatility

Publication:

Volatility as a Concept to Understand the Impact of Stress on the Microbiome

Resource Available:

https://github.com/thomazbastiaanssen/Volatility

Tjazi

Publication:

Bugs as Features (Part I): Concepts and Foundations for the Compositional Data Analysis of the Microbiome-Gut-Brain Axis

Resource Available:

https://github.com/thomazbastiaanssen/Tjazi

AURORA: AUtochthonous Random fOrest Random wAlk algorithm

Resource Available:

https://github.com/DalimilBujdos/aurora

Pacbio_methylome

Publication:

Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

Resource Available:

https://github.com/frbot/Pacbio-assemblies-and-methylome-analysis

Comparative genomics

Publication:

Comparative genomics and genotype-phenotype associations in Bifidobacterium breve

Resource Available:

https://github.com/frbot/Comparative-genomics

RNAseq analysis

Resource Available:

https://github.com/frbot/RNAseq

BlastXtract2

Publication:

BlastXtract2: Improving early exploration of (meta) genomes

Resource Available:

https://github.com/ClaessonLab/BlastXtract2

SPINGO: SPecies level IdentificatioN of metaGenOmic amplicons

Publication:

SPINGO: a rapid species-classifier for microbial amplicon sequences

Resource Available:

https://github.com/GuyAllard/SPINGO

GROND: Genome-derived Ribosomal OperoN Database

Publication:

GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences

Resource Available:

https://github.com/cazzlewazzle89/GROND

proGenomes v3

Publication:

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Resource Available:

https://progenomes.embl.de/

GMGC: the Global Microbial Gene Catalogue

Publication:

Towards the biogeography of prokaryotic genes

Resource Available:

https://gmgc.embl.de/

GMSC: the Global Microbial smORFs Catalogue

Publication:

A catalog of small proteins from the global microbiome

Resource Available:

https://gmsc.big-data-biology.org

AMPsphere

Publication:

Discovery of antimicrobial peptides in the global microbiome with machine learning

Resource Available:

https://ampsphere.big-data-biology.org/home

proMGE

Publication:

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Resource Available:

https://promge.embl.de/

MAPseq

Publication:

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

Resource Available:

https://github.com/jfmrod/MAPseq

Microbe Atlas Project

Resource Available:

https://microbeatlas.org/

treeclimbR

Publication:

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

Resource Available:

https://github.com/csoneson/treeclimbR