Bioinformatics Tools and Resources
High-throughput sequencing of nucleic acids has enabled researchers to quantitatively profile the composition of environmental and host-associated microbial communities. We have developed bioinformatic tools for taxonomic profiling, prophage detection and random barcoded transposon insertion data analysis as well as a global database of marine microbial genomes.
Ocean Microbiomics Database
Data repository to explore the diversity, biogeography and functions of microbes in the global ocean microbiome.
mBARq
Processing and analysis of barcoded mutant libraries for any transposon construct.
mOTUs
Profiling the taxonomic composition of microbial communities based on single-copy marker gene fragments in metagenomes.
mTAGs
Profiling the taxonomic composition of microbial communities based on 16S rRNA gene fragments (amplicons or metagenomes).
Read more about the tools on the external page microbiomics webpage.
Selected publications
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Dmitrijeva M*, Ruscheweyh HJ*, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, Zeller G, Sunagawa S✉
Nucleic Acids Res,53(D1), D797–D805, 2024. [external page DOI]
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 page DOI]
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 page DOI]
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 page DOI]
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 page DOI]
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 page DOI]