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

Phylogenetic comparative assembly

(2010) Peter Husemann et al.   Algorithms for Molecular Biology

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

A Genomic Survey of Positive Selection in Burkholderia pseudomallei Provides Insights into the Evolution of Accidental Virulence

(2010) Tannistha Nandi et al.   PLoS Pathogens

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

(2008) N. Nagarajan et al.   BIOINFORMATICS

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE