Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

Assembly complexity of prokaryotic genomes using short reads

(2010) Carl Kingsford et al.   BMC BIOINFORMATICS

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

(2010) Ali Bashir et al.   BMC GENOMICS

Complete genome sequence of Thermocrinis albus type strain (HI 11/12T)

(2010) Reinhard Wirth et al.   Standards in Genomic Sciences

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Maximum Likelihood Genome Assembly

(2009) Paul Medvedev et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

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

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