tag:joss.theoj.org,2005:/papers/tagged/samJournal of Open Source Software2023-10-23T10:25:02ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/44912023-09-12T20:03:28Z2023-09-13T00:01:13Zsamgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM)acceptedv0.6.22023-05-18 15:31:48 UTC892023-09-12 20:03:28 UTC820235663QiushengWuDepartment of Geography & Sustainability, University of Tennessee, Knoxville, TN 37996, United States0000-0001-5437-4073LucasPradoOscoFaculty of Engineering and Architecture and Urbanism, University of Western São Paulo, Rod. Raposo Tavares, km 572 - Limoeiro, Pres. Prudente 19067-175, SP, Brazil0000-0002-0258-536X10.21105/joss.05663https://doi.org/10.5281/zenodo.8338074Pythonhttps://joss.theoj.org/papers/10.21105/joss.05663.pdfgeospatial, segment anything, deep learning, satellitetag:joss.theoj.org,2005:Paper/36682023-06-22T18:20:23Z2023-06-23T00:01:38ZThe sspm R package for spatially-explicit surplus production population modelsacceptedv0.9.12022-06-21 14:30:02 UTC862023-06-22 18:20:23 UTC820234724ValentinLucetDepartment of Biology, Concordia University, Montreal, CA0000-0003-0268-818XEricJ.PedersenDepartment of Biology, Concordia University, Montreal, CA, Department of Biology, Memorial University of Newfoundland, St. John's, CA0000-0003-1016-540X10.21105/joss.04724https://doi.org/10.5281/zenodo.8015102Rhttps://joss.theoj.org/papers/10.21105/joss.04724.pdffisheries, management, modelling, GAMtag: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/29732022-01-29T00:44:59Z2022-01-30T00:01:17ZBam-readcount - rapid generation of basepair-resolution sequence metricsaccepted1.02021-08-15 14:11:57 UTC692022-01-29 00:44:59 UTC720223722AjayKhannaDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MODavidE.LarsonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Benson Hill, Inc. St. Louis, MOSridharNonavinkereSrivatsanDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MOMatthewMosiorDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Moffitt Cancer Center, Tampa, FLTravisE.AbbottMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Google, Inc. Mountain View, CASusannaKiwalaMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOTimothyJ.LeyDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOEricJ.DuncavageDepartment of Pathology, Washington University School of Medicine, St. Louis, MOMatthewJ.WalterDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOJasonR.WalkerMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOObiL.GriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOMalachiGriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOChristopherA.MillerDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO10.21105/joss.03722https://doi.org/10.5281/zenodo.5879149Rhttps://joss.theoj.org/papers/10.21105/joss.03722.pdfgenomics, cpp, sequencingtag:joss.theoj.org,2005:Paper/22882021-04-08T17:12:29Z2021-04-09T00:00:51ZPolSAR tools: A QGIS plugin for generating SAR descriptorsacceptedv0.62020-12-28 16:33:20 UTC602021-04-08 17:12:29 UTC620212970NarayanaraoBhogapurapuMicrowave Remote Sensing Lab, Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India0000-0002-6496-7283SubhadipDeyMicrowave Remote Sensing Lab, Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India0000-0002-4979-0192DipankarMandalMicrowave Remote Sensing Lab, Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India0000-0001-8407-7125AvikBhattacharyaMicrowave Remote Sensing Lab, Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India0000-0001-6720-6108Y.S.RaoMicrowave Remote Sensing Lab, Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India0000-0002-6351-239110.21105/joss.02970https://doi.org/10.5281/zenodo.4621292Pythonhttps://joss.theoj.org/papers/10.21105/joss.02970.pdfSAR, QGIS, Vegetation indices, Polarimetric decompositionstag:joss.theoj.org,2005:Paper/14612020-03-06T17:24:08Z2021-02-15T11:31:05Zcovtobed: a simple and fast tool to extract coverage tracks from BAM filesacceptedv1.0.02020-01-30 15:43:55 UTC472020-03-06 17:24:08 UTC520202119GiovanniBiroloDept. Medical Sciences, University of Turin, ITALYAndreaTelatinGut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, UK0000-0001-7619-281X10.21105/joss.02119https://doi.org/10.5281/zenodo.3695204C++https://joss.theoj.org/papers/10.21105/joss.02119.pdfbedtools, bamtools, genomics, bioinformatics, target enrichment, sequence coveragetag:joss.theoj.org,2005:Paper/5202018-08-09T14:54:41Z2021-02-15T11:33:18ZBAMnostic: an OS-agnostic toolkit for genomic sequence analysisaccepted0.8.42018-06-15 14:12:28 UTC282018-08-09 14:54:41 UTC32018826MarcusD.ShermanDepartment of Computational Medicine and Bioinformatics, University of Michigan0000-0002-0243-4609RyanE.MillsDepartment of Computational Medicine and Bioinformatics, University of Michigan, Department of Human Genetics, University of Michigan0000-0003-3425-699810.21105/joss.00826https://doi.org/10.5281/zenodo.1341915Pythonhttps://joss.theoj.org/papers/10.21105/joss.00826.pdfgenomics, bam, genetics, Next-Generation Sequencing