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.
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).
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 pageDOIcall_made]
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 pageDOIcall_made]
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 pageDOIcall_made]
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 pageDOIcall_made]
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 pageDOIcall_made]