Tools for mapping high-throughput sequencing data

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

(2012) Yanju Zhang et al.   BIOINFORMATICS

SEQanswers: an open access community for collaboratively decoding genomes

(2012) Jing-Woei Li et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Comparison of alignment software for genome-wide bisulphite sequence data

(2012) Aniruddha Chatterjee et al.   NUCLEIC ACIDS RESEARCH

X-MATE: a flexible system for mapping short read data

(2011) David L. A. Wood et al.   BIOINFORMATICS

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

(2011) Gregory R. Grant et al.   BIOINFORMATICS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

(2011) Songbo Huang et al.   Frontiers in Genetics

Supersplat--spliced RNA-seq alignment

(2010) D. W. Bryant et al.   BIOINFORMATICS

High quality SNP calling using Illumina data at shallow coverage

(2010) N. Malhis et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

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

(2010) Faraz Hach et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

MOM: maximum oligonucleotide mapping

(2009) H. L. Eaves et al.   BIOINFORMATICS

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

(2009) You Jung Kim et al.   BIOINFORMATICS

MicroRazerS: rapid alignment of small RNA reads

(2009) A.-K. Emde et al.   BIOINFORMATICS

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

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

(2009) Nicole Cloonan 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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

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

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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 DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

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

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

(2008) N. Malhis et al.   BIOINFORMATICS

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

PatMaN: rapid alignment of short sequences to large databases

(2008) Kay Prüfer 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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS