@article{Gruning_Yusuf-SARS_CoV_2_submission_ENA_Bioinformatics2021,
author = {Roncoroni, Miguel and Droesbeke, Bert and Eguinoa, Ignacio and De
          Ruyck, Kim and D'Anna, Flora and Yusuf, Dilmurat and Grüning,
          Björn and Backofen, Rolf and Coppens, Frederik},
title = {A {SARS-CoV-2} sequence submission tool for the European
         Nucleotide Archive},
journal = {Bioinformatics},
year = {2021},
doi = {10.1093/bioinformatics/btab421},
user = {cuyghur},
month = {jun},
language = {en},
issn = {1367-4803},
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).}
}