tag:joss.theoj.org,2005:/papers/tagged/metagenomicsJournal of Open Source Software2024-03-25T09:10:44ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/48632023-12-19T12:19:57Z2024-01-11T16:55:09ZMiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysisacceptedv0.52023-10-23 15:45:54 UTC922023-12-19 12:19:57 UTC820236038AdrienTaudièreIdEst, Saint-Bonnet-de-Salendrinque, 30460 France0000-0003-1088-118210.21105/joss.06038https://doi.org/10.5281/zenodo.10370781Rhttps://joss.theoj.org/papers/10.21105/joss.06038.pdfBioinformatic, Metagenomics, Barcoding, Reproducibilitytag:joss.theoj.org,2005:Paper/45792023-07-11T15:34:01Z2023-07-14T13:35:51ZTAXPASTA: TAXonomic Profile Aggregation and STAndardisationaccepted0.4.02023-07-05 17:39:09 UTC872023-07-11 15:34:01 UTC820235627MoritzE.BeberUnseen Bio ApS, Copenhagen, Denmark0000-0003-2406-1978MaximeBorryMicrobiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany0000-0001-9140-7559SofiaStamouliDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden0009-0006-0893-3771JamesA. FellowsYatesMicrobiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany, Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany0000-0001-5585-627710.21105/joss.05627https://doi.org/10.5281/zenodo.8105840https://joss.theoj.org/papers/10.21105/joss.05627.pdfbioinformatics, metagenomics, profiling, classification, standardisation, taxonomy, Pythontag:joss.theoj.org,2005:Paper/38582023-02-20T17:45:21Z2023-04-18T07:24:31ZMetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysisacceptedv.1.0.02022-09-08 01:21:00 UTC822023-02-20 17:45:21 UTC820234851BabakShabanMelbourne Data Analytics Platform, The University of Melbourne0000-0002-7393-810XMaria del MarQuirogaMelbourne Data Analytics Platform, The University of Melbourne0000-0002-8943-2808RobertTurnbullMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1274-6750EdoardoTescariMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1157-4897Kim-AnhLêCaoSchool of Mathematics and Statistics, Melbourne Integrative Genomics, The University of Melbourne0000-0003-3923-1116HeroenVerbruggenSchool of BioSciences, The University of Melbourne0000-0002-6305-474910.21105/joss.04851https://doi.org/10.26188/22032425wdl, Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04851.pdfmetagenomics, WDL, Singularity, Containerizationtag:joss.theoj.org,2005:Paper/39452022-12-28T09:07:11Z2022-12-29T00:01:16ZMetagenomic classification with KrakenUniq on low-memory computersacceptedv1.0.12022-10-06 17:50:41 UTC802022-12-28 09:07:11 UTC720224908ChristopherPockrandtCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAAlekseyV.ZiminCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAStevenL.SalzbergCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA10.21105/joss.04908https://doi.org/10.5281/zenodo.7459217Perlhttps://joss.theoj.org/papers/10.21105/joss.04908.pdfmetagenomics, classification, speciestag:joss.theoj.org,2005:Paper/35112022-06-01T20:05:57Z2022-06-02T00:01:04Zsam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment filesacceptedv1.0.0b2022-04-21 15:14:38 UTC742022-06-01 20:05:57 UTC720224360MaximeBorryMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany0000-0001-9140-7559AlexanderHübnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany0000-0003-3572-9996ChristinaWarinnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany, Department of Anthropology, Harvard University, Cambridge, MA, United States of America0000-0002-4528-587710.21105/joss.04360https://doi.org/10.5281/zenodo.6585307Pythonhttps://joss.theoj.org/papers/10.21105/joss.04360.pdfmetagenomics, microbiome, alignment, sam, bam, cram, htslib, taxonomy, LCA, ancestortag:joss.theoj.org,2005:Paper/29822021-10-27T15:45:53Z2021-10-28T00:06:23ZOpfi: A Python package for identifying gene clusters in large genomics and metagenomics data setsaccepted0.1.02021-08-20 03:05:15 UTC662021-10-27 15:45:53 UTC620213678AlexisM.HillDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USAJamesR.RybarskiDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USAKuangHuDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USAIlyaJ.FinkelsteinDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USAClausO.WilkeDepartment of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA10.21105/joss.03678https://doi.org/10.5281/zenodo.5601741Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.03678.pdfbioinformatics, metagenomics, gene cluster analysistag:joss.theoj.org,2005:Paper/16212021-04-16T18:17:11Z2021-04-17T15:55:53ZSneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read dataacceptedv0.9.102020-05-20 18:19:53 UTC602021-04-16 18:17:11 UTC620212334TaylorGriswoldEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USACurtisKapsakEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA, Weems Design Studio, Inc., Suwanee, GA, USA0000-0002-8735-1190JessicaC.ChenEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USAHenkC. denBakkerCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-4086-1580GrantWilliamsEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USAAlyssaKelleyWeems Design Studio, Inc., Suwanee, GA, USA, Waterborne Disease Prevention Branch (WDPB), Centers for Disease Control and Prevention, Atlanta, GA, USAEshawVidyaprakashEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA, IHRC, Atlanta, GA, USALeeS.KatzEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA, Center for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-2533-916110.21105/joss.02334https://doi.org/10.5281/zenodo.4657026Perl, Python, Prologhttps://joss.theoj.org/papers/10.21105/joss.02334.pdfQA/QCtag:joss.theoj.org,2005:Paper/21392021-01-08T09:10:54Z2021-02-15T11:29:47ZEUKulele: Taxonomic annotation of the unsung eukaryotic microbesacceptedv1.0.02020-10-29 10:55:19 UTC572021-01-08 09:10:54 UTC620212817AriannaI.KrinosBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, MIT-WHOI Joint Program in Oceanography, Cambridge and Woods Hole, MA, USA0000-0001-9767-8392SarahK.HuMarine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA0000-0002-4439-1360NatalieR.CohenMarine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA0000-0001-6156-9186HarrietAlexanderBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA0000-0003-1308-800810.21105/joss.02817https://doi.org/10.5281/zenodo.4422091Pythonhttps://joss.theoj.org/papers/10.21105/joss.02817.pdfTaxonomy, Metagenomics, Metatranscriptomics