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

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

(2014) Yonatan H Grad et al.   LANCET INFECTIOUS DISEASES

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

GAM-NGS: genomic assemblies merger for next generation sequencing

(2013) Riccardo Vicedomini et al.   BMC BIOINFORMATICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

(2013) Sara El-Metwally et al.   PLoS Computational Biology

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

(2013) Dale Muzzey et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

CLEVER: clique-enumerating variant finder

(2012) Tobias Marschall et al.   BIOINFORMATICS

SEQuel: improving the accuracy of genome assemblies

(2012) R. Ronen et al.   BIOINFORMATICS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Paired-end sequencing of Fosmid libraries by Illumina

(2012) L. J. S. Williams et al.   GENOME RESEARCH

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

Comparative genomic and proteomic analyses of PE/PPE multigene family of Mycobacterium tuberculosis H37Rv and H37Ra reveal novel and interesting differences with implications in virulence

(2012) Sakshi Kohli et al.   NUCLEIC ACIDS RESEARCH

Independent Large Scale Duplications in Multiple M. tuberculosis Lineages Overlapping the Same Genomic Region

(2012) Brian Weiner et al.   PLoS One

Comparative Analysis of Mycobacterium tuberculosis pe and ppe Genes Reveals High Sequence Variation and an Apparent Absence of Selective Constraints

(2012) Christopher R. E. McEvoy et al.   PLoS One

Conserved Immune Recognition Hierarchy of Mycobacterial PE/PPE Proteins during Infection in Natural Hosts

(2012) H. Martin Vordermeier et al.   PLoS One

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing

(2012) Chris Ford et al.   TUBERCULOSIS

GenomeView: a next-generation genome browser

(2011) T. Abeel et al.   NUCLEIC ACIDS RESEARCH

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Variation among Genome Sequences of H37Rv Strains of Mycobacterium tuberculosis from Multiple Laboratories

(2010) T. R. Ioerger et al.   JOURNAL OF BACTERIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

(2008) T. Abeel et al.   BIOINFORMATICS

Frequent Homologous Recombination Events in Mycobacterium tuberculosis PE/PPE Multigene Families: Potential Role in Antigenic Variability

(2008) A. Karboul et al.   JOURNAL OF BACTERIOLOGY