Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

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

(2012) Zamin Iqbal et al.   NATURE GENETICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Two Efficient Algorithms for Linear Time Suffix Array Construction

(2010) Ge Nong et al.   IEEE TRANSACTIONS ON COMPUTERS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

(2010) Nils Homer et al.   GENOME BIOLOGY

SNP-o-matic

(2009) Heinrich Magnus Manske et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski 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