@ARTICLE{Gruning_Yusuf-SARS_CoV_2_submission_ENA_Bioinformatics2021,
  title    = "A {SARS-CoV-2} sequence submission tool for the European
              Nucleotide Archive",
  author   = "Roncoroni, Miguel and Droesbeke, Bert and Eguinoa, Ignacio and De
              Ruyck, Kim and D'Anna, Flora and Yusuf, Dilmurat and Gr{\"u}ning,
              Bj{\"o}rn and Backofen, Rolf and Coppens, Frederik",
  abstract = "SUMMARY: Many aspects of the global response to the COVID-19
              pandemic are enabled by the fast and open publication of
              SARS-CoV-2 genetic sequence data. The European Nucleotide Archive
              (ENA) is the European recommended open repository for genetic
              sequences. In this work, we present a tool for submitting raw
              sequencing reads of SARS-CoV-2 to ENA. The tool features a
              single-step submission process, a graphical user interface,
              tabular-formatted metadata and the possibility to remove human
              reads prior to submission. A Galaxy wrap of the tool allows users
              with little or no bioinformatic knowledge to do bulk sequencing
              read submissions. The tool is also packed in a Docker container
              to ease deployment. AVAILABILITY: CLI ENA upload tool is
              available at github.com/usegalaxy-eu/ena-upload-cli (DOI
              10.5281/zenodo.4537621); Galaxy ENA upload tool at
              toolshed.g2.bx.psu.edu/view/iuc/ena\_upload/382518f24d6d and
              https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena\_upload
              (development) and; ENA upload Galaxy container at
              github.com/ELIXIR-Belgium/ena-upload-container (DOI
              10.5281/zenodo.4730785).",
  journal  = "Bioinformatics",
  month    =  jun,
  year     =  2021,
  language = "en",
  doi = "10.1093/bioinformatics/btab421",
  issn = "1367-4803",
  user = {cuyghur}
}