Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged Atosh

In the 2019 database issue, Nucleic Acids Research will include a new paper on the UNITE database for molecular identification of fungi (1). I have been involved in the development of UNITE in different ways since 2012, most prominently via the ITSx (2) and Atosh software which are ticking under the hood of the database.

In this update paper, we introduce a redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems. The database now contains around one million fungal ITS sequences that can be used for reference, which are clustered into roughly 459,000 species hypotheses (3). Each species hypothesis is assigned a digital object identifier (DOI), which enables unambiguous reference across studies. The paper is available as open access and the UNITE database is available open source from here.

References

  1. Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K: The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, Advance article, gky1022 (2018). doi: 10.1093/nar/gky1022
  2. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Souza F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. Methods in Ecology and Evolution, 4, 10, 914–919 (2013). doi: 10.1111/2041-210X.12073
  3. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TT, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Senés C, Smith ME, Suija A, Taylor DE, Telleria MT, Weiß M, Larsson KH: Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22, 21, 5271–5277 (2013). doi: 10.1111/mec.12481

I would like to sincerely apologize for that I have been terrible at responding to support issues pertaining to ITSx, Metaxa, Atosh etc. lately. I am currently on 50% parental leave and at the same time I am wrapping up three first-author papers, organizing a workshop and preparing a talk. Thus, support issues has been lagging a bit behind the last weeks to be able to cope with everything else. I have been ticking off most (all?) of my support questions the last couple of days, but if I have any remaining issues that I have missed to reply to, please re-send them to me!

I will try to improve response times, but it is hard when I am working less than usual (also, note that I (strangely) don’t get paid for supporting software, so I have to do this on my “sparetime”). My aim is to respond within a few days, so if I have not done so, please resend your e-mail with a friendly reminder that you are waiting for my response. Reminding me will very likely put your question up the priority pile.

So, my advice to becoming dads is: Do take paternal leave. Do take a lot of it. Share responsibilities with your partner. Because what you get back is awesome. (And also you get a good reason not to answer support questions in time.) But finally, don’t plan to wrap up the last couple of year’s worth of work and arrange a conference at the same time as you take out paternal leave. That will only make you feel insufficient at all fronts.

Keep the spirit high!