Simulation-based comprehensive benchmarking of RNA-seq aligners

ContextMap 2: fast and accurate context-based RNA-seq mapping

(2015) Thomas Bonfert et al.   BMC BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Comparing reference-based RNA-Seq mapping methods for non-human primate data

(2014) Ashlee M Benjamin et al.   BMC GENOMICS

RNA-Seq Gene Profiling - A Systematic Empirical Comparison

(2014) Nuno A. Fonseca et al.   PLoS One

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds

(2013) Jie Wu et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

CRAC: an integrated approach to the analysis of RNA-seq reads

(2013) Nicolas Philippe et al.   GENOME BIOLOGY

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

(2012) Robert Lindner et al.   PLoS One

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

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

(2011) Songbo Huang et al.   Frontiers in Genetics

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

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

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

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

PlasmoDB: a functional genomic database for malaria parasites

(2008) C. Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH