TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

(2015) Ernest D Benavente et al.   BMC BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes

(2014) Andreas Steiner et al.   BMC GENOMICS

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

(2014) T. A. Kohl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis

(2014) Tao Luo et al.   TUBERCULOSIS

PolyTB: A genomic variation map for Mycobacterium tuberculosis

(2014) Francesc Coll et al.   TUBERCULOSIS

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study

(2014) Timothy M Walker et al.   Lancet Respiratory Medicine

Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data

(2013) Josephine M Bryant et al.   BMC INFECTIOUS DISEASES

Proposal of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Loci for Subtyping of Mycobacterium tuberculosis Beijing Isolates

(2013) C. Allix-Beguec et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

(2013) Josephine M Bryant et al.   Lancet Respiratory Medicine

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

(2012) Francesc Coll et al.   BIOINFORMATICS

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing

(2012) Chris Ford et al.   TUBERCULOSIS

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria

(2010) T. Weniger et al.   NUCLEIC ACIDS RESEARCH

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

(2009) Stefan Niemann et al.   PLoS One

Tuberculosis Drug Resistance Mutation Database

(2009) Andreas Sandgren et al.   PLOS MEDICINE

Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis

(2008) Y. Murase et al.   JOURNAL OF MEDICAL MICROBIOLOGY