Assembly of long error-prone reads using de Bruijn graphs

Immunoglobulin Classification Using the Colored Antibody Graph

(2016) Stefano R. Bonissone et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FinisherSC: a repeat-aware tool for upgradingde novoassembly using long reads

(2015) Ka-Kit Lam et al.   BIOINFORMATICS

Assembling short reads from jumping libraries with large insert sizes

(2015) Irina Vasilinetc et al.   BIOINFORMATICS

hybridSPAdes: an algorithm for hybrid assembly of short and long reads

(2015) Dmitry Antipov et al.   BIOINFORMATICS

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

(2015) Judith Risse et al.   GigaScience

Resolving complex tandem repeats with long reads

(2014) Ajay Ummat et al.   BIOINFORMATICS

ExSPAnder: a universal repeat resolver for DNA fragment assembly

(2014) A. D. Prjibelski et al.   BIOINFORMATICS

What is the difference between the breakpoint graph and the de Bruijn graph?

(2014) Yu Lin et al.   BMC GENOMICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Long-read, whole-genome shotgun sequence data for five model organisms

(2014) Kristi E Kim et al.   Scientific Data

Engineering Plant Disease Resistance Based on TAL Effectors

(2013) Sebastian Schornack et al.   Annual Review of Phytopathology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins

(2013) Erin L. Doyle et al.   TRENDS IN CELL BIOLOGY

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

SEQuel: improving the accuracy of genome assemblies

(2012) R. Ronen et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

(2011) Z. Li et al.   Briefings in Functional Genomics

Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.

(2011) A. J. Bogdanove et al.   JOURNAL OF BACTERIOLOGY

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

(2010) Son K. Pham et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

(2008) Steven L Salzberg et al.   BMC GENOMICS

In Vivo and In Vitro Trans-Acylation by BryP, the Putative Bryostatin Pathway Acyltransferase Derived from an Uncultured Marine Symbiont

(2008) Nicole B. Lopanik et al.   CHEMISTRY & BIOLOGY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

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

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

Total synthesis of bryostatin 16 using atom-economical and chemoselective approaches

(2008) Barry M. Trost et al.   NATURE

Automated de novo protein sequencing of monoclonal antibodies

(2008) Nuno Bandeira et al.   NATURE BIOTECHNOLOGY