On citing Trinity

[Kris Alavattam]

Hi Brian,

Thanks again for your super useful tools and all the help you provide to the community. I checked the Trinity repo and saw that users should cite these two papers if they use Trinity in their research:

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PubMed PMID: 21572440.

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. Open Access in PMC doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID:23845962.

In addition to these papers, is there anything else we should cite?

Thanks,

Kris

[Brian Haas]

Hi Kris,

If you use specific analyses supported by the Trinity toolkit that are
for diff expression, like edgeR or DESeq2, you'd want to cite those
specifically.

Just let me know if you have any other related questions and I can
help hunt down the citations. If you use Trinotate for annotation, we
have a table of references for software used:
https://github.com/Trinotate/Trinotate/wiki/Lit-References

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas