Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

PEPR: pipelines for evaluating prokaryotic references

(2016) Nathan D. Olson et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

DUDes: a top-down taxonomic profiler for metagenomics

(2016) Vitor C. Piro et al.   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Evaluating methods for purifying cyanobacterial cultures by qPCR and high-throughput Illumina sequencing

(2016) Karina Heck et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

(2016) Nicholas A. Bokulich et al.   mSystems

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

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

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen et al.   ISME Journal

Large-scale contamination of microbial isolate genomes by Illumina PhiX control

(2015) Supratim Mukherjee et al.   Standards in Genomic Sciences

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS

(2015) Martin S. Lindner et al.   PLoS One

Improved Multiple Displacement Amplification (iMDA) and Ultraclean Reagents

(2014) S Motley et al.   BMC GENOMICS

Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

(2014) S. Y. C. Tong et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

A Duplex PCR-Based Assay for Measuring the Amount of Bacterial Contamination in a Nucleic Acid Extract from a Culture of Free-Living Protists

(2013) Alan O. Marron et al.   PLoS One

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

When Is a Microbial Culture "Pure"? Persistent Cryptic Contaminant Escapes Detection Even with Deep Genome Sequencing

(2013) P. M. Shrestha et al.   mBio

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

European quality clearance of new microbiological diagnostics

(2012) M. Ieven et al.   CLINICAL MICROBIOLOGY AND INFECTION

Complete Sequence of the First Chimera Genome Constructed by Cloning the Whole Genome of Synechocystis Strain PCC6803 into the Bacillus subtilis 168 Genome

(2012) S. Watanabe et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

(2010) Francis C Weng et al.   BMC BIOINFORMATICS

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS