Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

(2012) Sophie Schbath et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

(2012) Yue Li et al.   NUCLEIC ACIDS RESEARCH

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

(2011) José Otero et al.   BMC GENOMICS

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Data structures and compression algorithms for high-throughput sequencing technologies

(2010) Kenny Daily et al.   BMC BIOINFORMATICS

Genome variation discovery with high-throughput sequencing data

(2010) A. V. Dalca et al.   BRIEFINGS IN BIOINFORMATICS

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

(2009) Nathan L. Clement et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-generation sequencing: applications beyond genomes

(2008) Samuel Marguerat et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Compressed indexing and local alignment of DNA

(2008) T. W. Lam 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

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang 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

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY