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

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

(2019) Alexa B. R. McIntyre et al.   Nature Communications

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

(2019) Samuel M Nicholls et al.   GigaScience

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

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

(2018) Nicholas D Sanderson et al.   BMC GENOMICS

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

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

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

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

Lack of Evidence for Plague or Anthrax on the New York City Subway

(2015) Joel Ackelsberg et al.   Cell Systems

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY