Bioinformatics Tools and Resources

High-throughput sequencing of nucleic acids (and amino acids) has enabled researchers to profile the taxonomic, genomic and transcriptomic composition of environmental and host-associated microbial communities. We are interested in developing bioinformatic tools for taxonomic profiling, prophage detection, taxonomic profiling, transposon analysis and providing a data resource with genomes.

Ocean Microbiomics Database

Data repository to explore the diversity, biogeography and functions of microbes in the global ocean microbiome.

external pageSearch through the database

mBARq

Processing and analysis of barcoded mutant libraries for any transposon construct.

external pagemBARq is on GitHub!

mOTUs

Profiling the taxonomic composition of microbial communities based on single-copy marker gene fragments in metagenomes.

external pagemOTUs is on GitHub!

mTAGs

Profiling the taxonomic composition of microbial communities based on 16S rRNA gene fragments (amplicons or metagenomes).

external pagemTAGs is on GitHub!

mVIRs

Localizing inducible prophages using NGS data.

external pagemVIRs is on GitHub!

Selected publications

mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants and isogenic strain populations

Sintsova A, Ruscheweyh HJ, Field CM, Feer L, Nguyen BD, Daniel B, Hardt WD, Vorholt JA, Sunagawa S✉
Bioinformatics: 40(2), btae078, 2024. [external pageDOI]

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes

Salazar G*, Ruscheweyh HJ*, Hildebrand F, Acinas SG, Sunagawa S✉
Bioinformatics: 38(1), 270-272, 2021. [external pageDOI]

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

Zünd M, Ruscheweyh HJ, Field CM, Meyer N, Cuenca M, Hoces D, Hardt WD, Sunagawa S✉
Microbiome: 9, 77, 2021. [external pageDOI]

Microbial abundance, activity and population genomic profiling with mOTUs2

Milanese A*, Mende DR*, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G✉ and Sunagawa S✉
Nat Commun: 10, 1014, 2019. [external pageDOI]

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F , Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A and Bork P✉
Nat Methods: 10(12), 1196-9, 2013. [external pageDOI]