ReferencesΒΆ
[Bowtie] | Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology (2009). Software homepage. |
[Cufflinks] | Trapnell et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology (2010); Roberts et al., Improving RNA-Seq expression estimates by correcting for fragment bias, Genome Biology (2011). 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. |