JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

PASTA: splice junction identification from RNA-Sequencing data

(2013) Shaojun Tang et al.   BMC BIOINFORMATICS

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

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

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Songbo Huang et al.   Frontiers in Genetics

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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