Fast and accurate short read alignment with Burrows–Wheeler transform

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1997 • 71,835 citations

The Sequence Alignment/Map format and SAMtools

2009 • 54,537 citations

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

2009 • 20,860 citations

Improved tools for biological sequence comparison.

1988 • 11,455 citations

<tt>BLAT</tt>—The <tt>BLAST</tt>-Like Alignment Tool

2002 • 8,153 citations

A Greedy Algorithm for Aligning DNA Sequences

2000 • 5,089 citations

Real-Time DNA Sequencing from Single Polymerase Molecules

2008 • 3,446 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

A Block-sorting Lossless Data Compression Algorithm

1994 • 2,369 citations

Database indexing for production MegaBLAST searches

2008 • 1,098 citations

Opportunistic data structures with applications

2002 • 1,034 citations

SSAHA: A Fast Search Method for Large DNA Databases

2001 • 972 citations

PatternHunter: faster and more sensitive homology search

2002 • 846 citations

CloudBurst: highly sensitive read mapping with MapReduce

2009 • 628 citations

SHRiMP: Accurate Mapping of Short Color-space Reads

2009 • 566 citations

SeqMap: mapping massive amount of oligonucleotides to the genome

2008 • 477 citations

Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching

2005 • 433 citations

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

2008 • 329 citations

The smallest automation recognizing the subwords of a text

1985 • 319 citations

ZOOM! Zillions of oligos mapped

2008 • 206 citations

Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching

2000 • 177 citations

RazerS—fast read mapping with sensitivity control

2009 • 155 citations

Compressed indexing and local alignment of DNA

2008 • 131 citations

PASS: a program to align short sequences

2009 • 121 citations

OASIS

2003 • 101 citations

A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays

2007 • 85 citations

Slider—maximum use of probability information for alignment of short sequence reads and SNP detection

2008 • 60 citations

MOM: maximum oligonucleotide mapping

2009 • 50 citations

Space-Efficient Whole Genome Comparisons with Burrows–Wheeler Transforms

2005 • 44 citations

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

2009 • 22 citations