Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

The use of taxon-specific reference databases compromises metagenomic classification

(2020) Vanessa R. Marcelino et al.   BMC GENOMICS

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

(2020) Bing Ma et al.   Nature Communications

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

(2020) Till R. Lesker et al.   Cell Reports

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

(2020) Karel Břinda et al.   Nature Microbiology

Diversity within species: interpreting strains in microbiomes

(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

Pan-GWAS of Streptococcus agalactiae Highlights Lineage-Specific Genes Associated with Virulence and Niche Adaptation

(2020) Andrea Gori et al.   mBio

Streptococcus thermophilus: To Survive, or Not to Survive the Gastrointestinal Tract, That Is the Question!

(2020) Anđela Martinović et al.   Nutrients

Assembly methods for nanopore-based metagenomic sequencing: a comparative study

(2020) Adriel Latorre-Pérez et al.   Scientific Reports

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

(2020) Ana Elena Pérez-Cobas et al.   Microbial Genomics

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data

(2020) Christine Anyansi et al.   Frontiers in Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

(2019) Alexander T. Dilthey et al.   Nature Communications

Improved representation of sequence Bloom trees

(2019) Robert S Harris et al.   BIOINFORMATICS

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

(2019) Marco Meola et al.   BMC GENOMICS

First Insight into the Probiotic Properties of Ten Streptococcus thermophilus Strains Based on In Vitro Conditions

(2019) Jie Zhang et al.   CURRENT MICROBIOLOGY

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

(2019) Voula Alexandraki et al.   Frontiers in Microbiology

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

(2018) Francois Balloux et al.   TRENDS IN MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

(2017) Märt Roosaare et al.   PeerJ

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

A large scale in vitro screening of Streptococcus thermophilus strains revealed strains with a high anti-inflammatory potential

(2016) Maira Junjua et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Spaced seeds improvek-mer-based metagenomic classification

(2015) Karel Břinda et al.   BIOINFORMATICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Konnector v2.0: pseudo-long reads from paired-end sequencing data

(2015) Benjamin P Vandervalk et al.   BMC Medical Genomics

Bloofi: Multidimensional Bloom filters

(2015) Adina Crainiceanu et al.   INFORMATION SYSTEMS

Fast alignment-free sequence comparison using spaced-word frequencies

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY