HISAT: a fast spliced aligner with low memory requirements

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

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP

(2011) J. R. Grant et al.   BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

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

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

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS