[Bowtie]Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology (2009). Software homepage.
[Ensembl]Flicek et al, Ensembl 2014, Nucleic Acids Research (2014). Ensembl homepage.
[eXpress]Roberts and Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods (2013). Software homepage.
[FluxSimulator]Griebel et al., Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Research (2012). Software homepage.
[Hansen]Hansen et al., Biases in Illumina transcriptome sequencing caused by random hexamer priming, Nucleic Acids Research (2010).
[Kallisto]Bray et al., Near-optimal RNA-Seq quantification, arxiv (2015). Software homepage.
[RSEM]Li and Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics (2011). Software homepage.
[Sailfish]Patro et al., Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms, Nature Biotechnology (2014). Software homepage.
[Salmon]Patro et al., Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment, bioarxiv (2015). Software homepage.
[SAM]Li et al., The Sequence alignment/map (SAM) format and SAMtools. SAMtools homepage.
[TopHat]Kim et al., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biology (2013). Software homepage.