BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

(2021) Meghan Maguire et al.   PLoS One

Freshwater monitoring by nanopore sequencing

(2021) Lara Urban et al.   eLife

Fast and sensitive taxonomic assignment to metagenomic contigs

(2021) M Mirdita et al.   BIOINFORMATICS

Genome-resolved metagenomics using environmental and clinical samples

(2021) Masood ur Rehman Kayani et al.   BRIEFINGS IN BIOINFORMATICS

Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples

(2021) Nick P. G. Gauthier et al.   PLoS One

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

(2020) R. A. Barco et al.   mBio

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

(2020) Nicholas D. Sanderson et al.   GENOME RESEARCH

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Considerations for diagnostic COVID-19 tests

(2020) Olivier Vandenberg et al.   NATURE REVIEWS MICROBIOLOGY

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

(2020) Dandan Lang et al.   GigaScience

Hypervirulent Klebsiella pneumoniae

(2019) Thomas A. Russo et al.   CLINICAL MICROBIOLOGY REVIEWS

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

(2019) Krithika Arumugam et al.   Microbiome

Advancing Genome-Resolved Metagenomics beyond the Shotgun

(2019) Rex R. Malmstrom et al.   mSystems

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

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

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

(2019) Lauren M. Petersen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

(2019) Teresa L. Street et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

(2018) Daniel H. Huson et al.   Biology Direct

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

AMBER: Assessment of Metagenome BinnERs

(2018) Fernando Meyer et al.   GigaScience

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

(2016) Ivan Gregor et al.   PeerJ

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS