tag:joss.theoj.org,2005:/papers/tagged/WGSJournal of Open Source Software2023-07-20T11:29:57ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/41882023-07-20T11:29:57Z2023-07-27T07:02:54ZSeqPanther: Sequence manipulation and mutation statistics toolsetacceptedv1.0.02023-02-03 07:59:06 UTC872023-07-20 11:29:57 UTC820235305JamesEmmanuelSanKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-5736-664XStephanievan WykCentre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2655-8518HouriiyahTegallyKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-7102-8540SimeonEcheYale University School of Medicine, New Haven, Connecticut, United States of America0000-0001-5494-8372EduanWilkinsonKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2503-9441AquillahM.KanziKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa0000-0001-6081-9438Tuliode OliveiraKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa, Department of Global Health, University of Washington, Seattle, WA, United States of America0000-0002-3027-5254AnmolM.KiranSchool of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland0000-0003-2680-230310.21105/joss.05305https://doi.org/10.5281/zenodo.8126922Pythonhttps://joss.theoj.org/papers/10.21105/joss.05305.pdfBioinformatics, sequence analysis, NGS, codon, amino acid substitution, nucleotide substitution, INDELtag:joss.theoj.org,2005:Paper/22052021-05-08T08:17:33Z2021-05-09T00:01:01Zbcdata: An R package for searching & retrieving data from the B.C. Data Catalogueaccepted0.2.12020-11-27 19:20:18 UTC612021-05-08 08:17:33 UTC620212927AndrewC.TeucherState of Environment Reporting, Ministry of Environment and Climate Change Strategy, Province of British Columbia0000-0002-7840-692XSamJ.AlbersData Science Partnerships, Ministry of Citizens' Services, Province of British Columbia0000-0002-9270-7884StephanieL.HazlittData Science Partnerships, Ministry of Citizens' Services, Province of British Columbia0000-0002-3161-230410.21105/joss.02927https://doi.org/10.5281/zenodo.4737824Rhttps://joss.theoj.org/papers/10.21105/joss.02927.pdfopen data, WFS, British Columbia, Canadatag:joss.theoj.org,2005:Paper/19282020-12-24T09:13:28Z2021-02-15T11:30:11Zqgs: A flexible Python framework of reduced-order multiscale climate modelsacceptedv0.2.02020-08-05 10:23:11 UTC562020-12-24 09:13:28 UTC520202597JonathanDemaeyerRoyal Meteorological Institute of Belgium, Avenue Circulaire, 3, 1180 Brussels, Belgium0000-0002-5098-404XLesleyDe CruzRoyal Meteorological Institute of Belgium, Avenue Circulaire, 3, 1180 Brussels, Belgium0000-0003-4458-8953StéphaneVannitsemRoyal Meteorological Institute of Belgium, Avenue Circulaire, 3, 1180 Brussels, Belgium0000-0002-1734-104210.21105/joss.02597https://doi.org/10.5281/zenodo.4368844Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.02597.pdfNumba, Idealized atmospheric model, Coupled model, Mid-latitude climate variabilitytag:joss.theoj.org,2005:Paper/14152020-02-04T14:47:33Z2021-02-15T11:31:13ZReferenceSeeker: rapid determination of appropriate reference genomesacceptedv1.42019-12-19 18:33:52 UTC462020-02-04 14:47:33 UTC520201994OliverSchwengersBioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, 35392, Germany, Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany0000-0003-4216-2721TorstenHainInstitute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, GermanyTrinadChakrabortyInstitute of Medical Microbiology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, GermanyAlexanderGoesmannBioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, 35392, Germany, German Centre for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany0000-0002-7086-256810.21105/joss.01994https://doi.org/10.5281/zenodo.3635630Pythonhttps://joss.theoj.org/papers/10.21105/joss.01994.pdfBioinformatics, WGS, NGS, Microbiologytag:joss.theoj.org,2005:Paper/3422018-02-08T11:29:57Z2021-02-15T11:33:44Zreper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genomeacceptedv1.0.02017-12-21 17:14:53 UTC222018-02-08 11:29:57 UTC32018527NiklasTerhoevenCenter for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität Würzburg0000-0002-8669-0000JörgSchultzCenter for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität WürzburgThomasHacklDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology0000-0002-0022-320X10.21105/joss.00527https://doi.org/10.5281/zenodo.1167969Perl, Rhttps://joss.theoj.org/papers/10.21105/joss.00527.pdfrepeats, transposons, kmer, pipeline, repeat landscape, NGStag:joss.theoj.org,2005:Paper/3602018-02-05T20:44:45Z2021-02-15T11:33:41ZCheckQC: Quick quality control of Illumina sequencing runsacceptedv1.2.02018-01-26 12:20:37 UTC222018-02-05 20:44:45 UTC32018556MatildaÅslinDepartment of Medical Sciences, Molecular Medicine and Science for Life Laboratory Uppsala University, Uppsala, Sweden0000-0002-2450-6415MonikaBrandtDepartment of Medical Sciences, Molecular Medicine and Science for Life Laboratory Uppsala University, Uppsala, Sweden0000-0002-8184-9465JohanDahlbergDepartment of Medical Sciences, Molecular Medicine and Science for Life Laboratory Uppsala University, Uppsala, Sweden0000-0001-6962-146010.21105/joss.00556https://doi.org/10.5281/zenodo.1166052Pythonhttps://joss.theoj.org/papers/10.21105/joss.00556.pdfillumina, ngs, quality control, mps, sequencingtag:joss.theoj.org,2005:Paper/2432017-08-30T00:00:00Z2021-02-15T11:34:00Z'Sequana': a Set of Snakemake NGS pipelinesaccepted0.4.12017-07-24 11:05:35 UTC162017-08-30 00:00:00 UTC22017352ThomasCokelaerInstitut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France, Institut Pasteur - Biomics Pole - Paris, France0000-0001-6286-1138DimitriDesvillechabrolInstitut Pasteur - Biomics Pole - Paris, France0000-0002-4947-7876RachelLegendreInstitut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France, Institut Pasteur - Biomics Pole - Paris, France0000-0002-5196-9431MélissaCardonInstitut Pasteur - Biomics Pole - Paris, France0000-0001-9906-323610.21105/joss.00352https://doi.org/10.5281/zenodo.853160Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.00352.pdfsnakemake, rna-seq, variant calling, taxonomy, denovo, pipeline, genome coverage