Removing contaminants from databases of draft genomes

EuPathDB: the eukaryotic pathogen genomics database resource

(2016) Cristina Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

Human Contamination in Public Genome Assemblies

(2016) Kirill Kryukov et al.   PLoS One

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

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

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

(2013) H. Hasman et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Recent progress and understanding of the molecular mechanisms of the rice-Magnaporthe oryzaeinteraction

(2010) JINLING LIU et al.   MOLECULAR PLANT PATHOLOGY

African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum

(2010) F. Prugnolle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA