The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

The Sequence Alignment/Map format and SAMtools

2009 • 54,537 citations

Fast and accurate short read alignment with Burrows–Wheeler transform

2009 • 51,582 citations

MapReduce

2008 • 18,382 citations

The Human Genome Browser at UCSC

2002 • 9,920 citations

Genome sequencing in microfabricated high-density picolitre reactors

2005 • 7,594 citations

dbSNP: the NCBI database of genetic variation

2001 • 6,995 citations

The International HapMap Project

2003 • 5,951 citations

Next-generation DNA sequencing

2008 • 4,262 citations

Accurate whole human genome sequencing using reversible terminator chemistry

2008 • 3,547 citations

SOAP: short oligonucleotide alignment program

2008 • 3,006 citations

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

2008 • 2,646 citations

The complete genome of an individual by massively parallel DNA sequencing

2008 • 1,792 citations

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

2009 • 1,447 citations

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

2009 • 1,376 citations

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

2009 • 1,279 citations

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

2009 • 1,207 citations

SSAHA: A Fast Search Method for Large DNA Databases

2001 • 972 citations

The diploid genome sequence of an Asian individual

2008 • 922 citations

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

2008 • 825 citations

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

2008 • 791 citations

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC

2006 • 756 citations

Computation for ChIP-seq and RNA-seq studies

2009 • 556 citations

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

2009 • 522 citations

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

2009 • 518 citations

Complete MHC Haplotype Sequencing for Common Disease Gene Mapping

2004 • 289 citations

Bayesian statistics in genetics: a guide for the uninitiated

1999 • 162 citations

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment

2009 • 52 citations