tag:joss.theoj.org,2005:/papers/tagged/genomesJournal of Open Source Software2024-03-27T15:29:57ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/49212024-03-27T15:29:57Z2024-03-28T11:12:37ZautoStreamTree: Genomic variant data fitted to geospatial networksacceptedv1.0.02023-11-06 11:25:49 UTC952024-03-27 15:29:57 UTC920246160TylerK.ChafinBiomathematics and Statistics Scotland, Edinburgh, United Kingdom0000-0001-8687-5905StevenM.Mussmann(current address) Abernathy Fish Technology Center, U.S. Fish & Wildlife Service, Longview, WA, United States of America, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America0000-0002-5237-5088MarlisR.DouglasDepartment of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America0000-0001-6234-3939MichaelE.DouglasDepartment of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America0000-0001-9670-782510.21105/joss.06160https://doi.org/10.5281/zenodo.10866066Pythonhttps://joss.theoj.org/papers/10.21105/joss.06160.pdfriverscape genomics, geo-genetic patterns, population geneticstag:joss.theoj.org,2005:Paper/48492024-03-25T09:10:44Z2024-03-26T00:00:59ZAcanthophis: a comprehensive plant hologenomics pipelineacceptedv1.0.02023-10-15 07:16:35 UTC952024-03-25 09:10:44 UTC920246062KevinD.MurrayMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2466-1917JustinO.BorevitzResearch School of Biology, Australian National University, Canberra, Australia0000-0001-8408-3699DetlefWeigelMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2114-7963NormanWarthmannResearch School of Biology, Australian National University, Canberra, Australia, FAO/IAEA Joint Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Laboratory, Seibersdorf, Austria0000-0002-1178-840910.21105/joss.06062https://doi.org/10.5281/zenodo.10795245Pythonhttps://joss.theoj.org/papers/10.21105/joss.06062.pdfpython, snakemake, plants, metagenomics, variant calling, population genomics, reference-free classificationtag:joss.theoj.org,2005:Paper/49682024-02-27T21:44:24Z2024-02-28T00:01:10ZKoverage: Read-coverage analysis for massive (meta)genomics datasetsaccepted0.1.72023-11-30 06:28:29 UTC942024-02-27 21:44:24 UTC920246235MichaelJ.RoachFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia, Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia0000-0003-1488-5148BradleyJ.HartHealth and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA, Australia0000-0001-8110-2460SarahJ.BeecroftPawsey Supercomputing Research Centre, Kensington, WA, Australia0000-0002-3935-2279BhavyaPapudeshiFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia0000-0001-5359-3100LauraK.InglisFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia0000-0001-7919-8563SusannaR.GrigsonFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia0000-0003-4738-3451VijiniMallawaarachchiFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia0000-0002-2651-8719GeorgeBourasAdelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia, The Department of Surgery – Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, SA, Australia0000-0002-5885-4186RobertA.EdwardsFlinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia0000-0001-8383-894910.21105/joss.06235https://doi.org/10.5281/zenodo.10633263Pythonhttps://joss.theoj.org/papers/10.21105/joss.06235.pdfSnakemake, Genomics, Metagenomicstag:joss.theoj.org,2005:Paper/48382024-01-22T15:00:12Z2024-01-23T11:55:19Zcstag and cstag-cli: tools for manipulating and visualizing cs tagsacceptedv1.0.42023-10-06 03:25:34 UTC932024-01-22 15:00:12 UTC920246066AkihiroKunoDepartment of Anatomy and Embryology, University of Tsukuba, Tsukuba, Ibaraki, Japan, Laboratory Animal Resource Center, Trans-border Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.0000-0002-4674-688210.21105/joss.06066https://doi.org/10.5281/zenodo.10544838Pythonhttps://joss.theoj.org/papers/10.21105/joss.06066.pdfpython, genomics, sequencing, bioinformaticstag:joss.theoj.org,2005:Paper/46842024-01-11T17:19:49Z2024-01-12T00:01:11ZDnaapler: A tool to reorient circular microbial genomesacceptedv0.2.02023-08-09 03:49:48 UTC932024-01-11 17:19:49 UTC920245968GeorgeBourasAdelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia, The Department of Surgery – Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia0000-0002-5885-4186SusannaR.GrigsonFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia0000-0003-4738-3451BhavyaPapudeshiFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia0000-0001-5359-3100VijiniMallawaarachchiFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia0000-0002-2651-8719MichaelJ.RoachFlinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, South Australia 5042, Australia, Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia0000-0003-1488-514810.21105/joss.05968https://doi.org/10.5281/zenodo.10251242Just, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05968.pdfmicrobiology, genomicstag:joss.theoj.org,2005:Paper/44622023-11-01T16:34:42Z2023-11-02T00:00:44ZGGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samplesacceptedv1.0.02023-05-01 13:29:12 UTC912023-11-01 16:34:42 UTC820235687Che-WeiChangUniversity of Hohenheim, Stuttgart, Germany0000-0001-6704-3732KarlSchmidUniversity of Hohenheim, Stuttgart, Germany0000-0001-5129-895X10.21105/joss.05687https://doi.org/10.6084/m9.figshare.24438388Rhttps://joss.theoj.org/papers/10.21105/joss.05687.pdflandscape genomics, K nearest neighbors, geo-genetic patternstag:joss.theoj.org,2005:Paper/42822023-10-23T10:25:02Z2023-10-24T00:01:06ZQuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Dataaccepted1.32023-03-06 22:06:16 UTC902023-10-23 10:25:02 UTC820235313ManavalanGajapathyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8606-0113BrandonM.WilkCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4110-2324ElizabethA.WortheyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0003-4083-776410.21105/joss.05313https://doi.org/10.5281/zenodo.10002036Jinja, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05313.pdfsnakemake, quality control, genome sequencing, exome sequencing, QC review, multiqc, singularity, bam, vcftag:joss.theoj.org,2005:Paper/42982023-10-19T10:05:08Z2023-10-20T00:00:55ZBaargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistanceacceptedv0.12023-03-10 09:09:20 UTC902023-10-19 10:05:08 UTC820235397JulietteHayerMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0003-4899-9637JacquesDainatMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France0000-0002-6629-0173EllaMarcyMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Centre Hospitalier Universitaire (CHU) Lapeyronie, Montpellier, France0009-0002-6000-1665Anne-LaureBañulsMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0002-2106-866710.21105/joss.05397https://doi.org/10.5281/zenodo.8386399Python, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.05397.pdfWhole Genome Shotgun, Genomics, Long reads sequencing technology, Short reads sequencing technology, Antimicrobial Resistance, Pangenometag:joss.theoj.org,2005:Paper/42862023-10-01T20:53:57Z2023-10-02T07:50:01ZRosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modelingaccepted0.6.02023-03-07 19:18:39 UTC902023-10-01 20:53:57 UTC820235443AngelinaE.Uno-AntonisonCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4631-9135RababFatimaCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-3739-6331JamesSchererCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4272-2082AlexanderMossCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0001-5112-0270DonnaBrownCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8805-7225AleksandraFoksinskaHugh Kaul Precision Medicine Institute, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-1035-3294ManavalanGajapathyCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8606-0113ElizabethJ.WilkDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-7078-1215BrittanyN.LasseigneDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-1642-8904ElizabethWortheyCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0003-4083-776410.21105/joss.05443https://doi.org/10.5281/zenodo.8380641Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05443.pdfanimal modeling, rare disease, diagnosis, genomics, phenotype, python, javascript, web applicationtag:joss.theoj.org,2005:Paper/41792023-05-10T21:48:40Z2023-05-11T09:01:03Zmutyper: assigning and summarizing mutation types for analyzing germline mutation spectraacceptedv0.7.02023-01-24 22:40:00 UTC852023-05-10 21:48:40 UTC820235227WilliamS.DeWittDepartment of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, United States of America0000-0002-6802-9139LukeZhuDepartment of Bioengineering, University of Washington, Seattle, WA, United States of America0000-0002-6324-1464MitchellR.VollgerDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-8651-1615MichaelE.GoldbergDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America, Departments of Human Genetics and of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States of America0000-0003-3310-6349AndreaTalentiThe Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom0000-0003-1309-3667AnnabelC.BeichmanDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-6991-587XKelleyHarrisDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0003-0302-252310.21105/joss.05227https://doi.org/10.5281/zenodo.7921769Pythonhttps://joss.theoj.org/papers/10.21105/joss.05227.pdfgenomics, computational biology, bioinformatics, mutation spectrum, python