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

A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni

(2012) Anna V. Protasio et al.   PLoS Neglected Tropical Diseases

Graph accordance of next-generation sequence assemblies

(2011) G. Yao et al.   BIOINFORMATICS

Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors

(2011) Simon Heilbronner et al.   FEMS MICROBIOLOGY LETTERS

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

(2011) M. B. Rogers et al.   GENOME RESEARCH

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

(2011) T. Downing et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

RATT: Rapid Annotation Transfer Tool

(2011) Thomas D. Otto et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Cestode genomics - progress and prospects for advancing basic and applied aspects of flatworm biology

(2011) P. D. OLSON et al.   PARASITE IMMUNOLOGY

Genotypic and Phenotypic Modifications of Neisseria meningitidis after an Accidental Human Passage

(2011) Hélène Omer et al.   PLoS One

Comparing De Novo Genome Assembly: The Long and Short of It

(2011) Giuseppe Narzisi et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux

(2011) Nicola K. Petty et al.   PLoS Pathogens

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

(2010) Thomas D. Otto et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

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

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

SNP-o-matic

(2009) Heinrich Magnus Manske et al.   BIOINFORMATICS

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

(2009) Richard A Stabler et al.   GENOME BIOLOGY

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS