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seqan / seqan

SeqAn's official repository.
https://www.seqan.de
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Citing packages (e.g. Yara) #2105

Closed klmr closed 7 years ago

klmr commented 7 years ago

Hi, I’m using YARA (in conjunction with SLIMM) in my workflow. However, it doesn’t seem to be published separately. How should I cite it in our publication? Relatedly, how should I cite recent versions of SeqAn? The original publication is rather dated and doesn’t acknowledge any of the recent authors’ contributions.

smehringer commented 7 years ago

Hi @klmr, thanks for using SeqAn.

Unfortunately @esiragusa has not published YARA yet, so I think it's fine to reference to the GitHub page (https://github.com/seqan/seqan/tree/master/apps/yara) and cite SeqAn.

As you asked, we actually got accepted into the Journal of Biotechnology last month with the current state of our library. Title: The SeqAb C++ template library for efficient sequence analysis: A resource for programmers by Knut Reinert; Marcel Ehrhardt; Hannes Hauswedell; Svenja Mehringer; René Rahn; Jongkyu Kim; Christopher Pockrandt; Jörg Winkler; Enrico Siragusa, Dr.; Gianvito Urgese; David Weese, Dr.; Temesgen Dadi SI: de.NBI Journal of Biotechnology (accepted 2017)

I'm not sure when the article will be released but we will update the citation information on our website and on Github as soon as it is out.

esiragusa commented 7 years ago

Hey Konrad! As Svenja said, there is no journal article describing the latest Yara. However you can use one of these two references here: my dissertation describes the latest version of Yara, while the NAR paper describes an older version.

klmr commented 7 years ago

So, to clarify, the Masai paper describes an earlier version of Yara? Cool, didn’t know that.