ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

(2012) A. A. Gritsenko et al.   BIOINFORMATICS

Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on De Novo Assembly via a Combinatorial Sequencing Strategy

(2012) B. Tang et al.   JOURNAL OF BACTERIOLOGY

Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms

(2012) Minjun Yang et al.   PLoS One

Visualization and quality assessment of de novo genome assemblies

(2011) Oksana Riba-Grognuz et al.   BIOINFORMATICS

Fast scaffolding with small independent mixed integer programs

(2011) L. Salmela et al.   BIOINFORMATICS

Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles

(2011) Xiao-Yan You et al.   EXTREMOPHILES

Whole Genome Sequence of the Rifamycin B-Producing Strain Amycolatopsis mediterranei S699

(2011) M. Verma et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain Po82

(2011) J. Xu et al.   JOURNAL OF BACTERIOLOGY

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

(2011) Song Gao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation

(2011) Shuang Mi et al.   JOURNAL OF MICROBIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Complete Genome Sequence of Mycoplasma bovis Strain Hubei-1

(2011) Yuan Li et al.   PLoS One

Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome

(2011) Ya-feng Chen et al.   VIROLOGY

Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine

(2011) Peng Zheng et al.   GENOME BIOLOGY

Gap5—editing the billion fragment sequence assembly

(2010) James K. Bonfield et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Complete Genome Sequence of Bacillus thuringiensis Mutant Strain BMB171

(2010) J. He et al.   JOURNAL OF BACTERIOLOGY

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

EagleView: A genome assembly viewer for next-generation sequencing technologies

(2008) W. Huang et al.   GENOME RESEARCH