A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

(2010) Robert W Blakesley et al.   BMC GENOMICS

Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine

(2009) Tracy Tucker et al.   AMERICAN JOURNAL OF HUMAN GENETICS

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

(2009) Burkhard Steuernagel et al.   BMC GENOMICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

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

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

(2009) R. Li et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

(2008) I. Hajirasouliha et al.   BIOINFORMATICS

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

(2008) Brian D. Ondov et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

An MCMC algorithm for haplotype assembly from whole-genome sequence data

(2008) V. Bansal et al.   GENOME RESEARCH

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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

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

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Parallel tagged sequencing on the 454 platform

(2008) Matthias Meyer et al.   Nature Protocols

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS