List of RNA-Seq bioinformatics tools

RNA-Seq^[1]^[2]^[3] is a technique^[4] that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. Here are listed some of the principal tools commonly employed and links to some important web resources.

^ Wang Z, Gerstein M, Snyder M (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews. Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.
^ Kukurba KR, Montgomery SB (April 2015). "RNA Sequencing and Analysis". Cold Spring Harbor Protocols. 2015 (11): 951–969. doi:10.1101/pdb.top084970. PMC 4863231. PMID 25870306.
^ Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. (January 2016). "A survey of best practices for RNA-seq data analysis". Genome Biology. 17 (13): 13. doi:10.1186/s13059-016-0881-8. PMC 4728800. PMID 26813401.
^ "RNA Sequencing and analysis" (PDF). Canadian Bioinformatics Workshops. 2012.

[Wang2009-1] Wang Z, Gerstein M, Snyder M (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews. Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.

[Kimberley2015-2] Kukurba KR, Montgomery SB (April 2015). "RNA Sequencing and Analysis". Cold Spring Harbor Protocols. 2015 (11): 951–969. doi:10.1101/pdb.top084970. PMC 4863231. PMID 25870306.

[Ana2016-3] Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. (January 2016). "A survey of best practices for RNA-seq data analysis". Genome Biology. 17 (13): 13. doi:10.1186/s13059-016-0881-8. PMC 4728800. PMID 26813401.

[CA2012-4] "RNA Sequencing and analysis" (PDF). Canadian Bioinformatics Workshops. 2012.

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