tag:joss.theoj.org,2005:/papers/tagged/VCFJournal 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/39072022-12-23T18:24:34Z2022-12-24T00:00:58ZGLUE Code: A framework handling communication and interfaces between scalesacceptedv1.0.02022-09-20 21:01:36 UTC802022-12-23 18:24:34 UTC720224822AleksandraPachalievaCenter for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA, Earth and Environmental Sciences (EES) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0003-1246-0410RobertS.PavelComputer, Computational and Statistical Sciences (CCS) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0001-7913-9918JavierE.SantosCenter for Non-Linear Studies, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA, Earth and Environmental Sciences (EES) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0002-2404-3975AbdourahmaneDiawFusion Energy Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA0000-0001-6743-3255NicholasLubbersComputer, Computational and Statistical Sciences (CCS) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0002-9001-9973MohamedMehanaEarth and Environmental Sciences (EES) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0003-2472-2879JeffreyR.HaackComputer, Computational and Statistical Sciences (CCS) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0002-2044-0885HariS.ViswanathanEarth and Environmental Sciences (EES) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0002-1178-9647DanielLivescuComputer, Computational and Statistical Sciences (CCS) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0003-2367-1547TimothyC.GermannTheoretical Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0002-6813-238XChristophJunghansComputer, Computational and Statistical Sciences (CCS) Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA0000-0003-0925-145810.21105/joss.04822https://doi.org/10.5281/zenodo.7469110Fortran, C++, C, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04822.pdfmultiscale simulations, active machine leanring, scale-bridging, ICF, MDtag:joss.theoj.org,2005:Paper/19162020-10-12T12:31:13Z2021-02-15T11:30:12Zcfdm: A Python reference implementation of the CF data modelaccepted1.8.6.02020-07-28 13:30:43 UTC542020-10-12 12:31:13 UTC520202717DavidHassellNational Centre for Atmospheric Science, UK, University of Reading, UK0000-0001-5106-7502SadieL.BartholomewNational Centre for Atmospheric Science, UK, University of Reading, UK0000-0002-6180-360310.21105/joss.02717https://doi.org/10.5281/zenodo.4075077Pythonhttps://joss.theoj.org/papers/10.21105/joss.02717.pdfCF, metadata, climate, meteorology, oceanographytag:joss.theoj.org,2005:Paper/18022020-10-01T19:54:19Z2021-02-15T11:30:25Zcerebra: A tool for fast and accurate summarizing of variant calling format (VCF) filesacceptedv1.1.02020-06-25 17:55:14 UTC542020-10-01 19:54:19 UTC520202432LincolnHarrisChan Zuckerberg Biohub, San Francisco, CA, United States0000-0003-2544-4225RohanVanheusdenChan Zuckerberg Biohub, San Francisco, CA, United StatesOlgaBotvinnikChan Zuckerberg Biohub, San Francisco, CA, United States0000-0003-4412-7970SpyrosDarmanisChan Zuckerberg Biohub, San Francisco, CA, United States0000-0003-4002-815810.21105/joss.02432https://doi.org/10.5281/zenodo.4050557Pythonhttps://joss.theoj.org/papers/10.21105/joss.02432.pdfpython, genomics, variant calling, VCF, single-cell, cancertag:joss.theoj.org,2005:Paper/7352019-03-26T06:29:14Z2021-02-15T11:32:46Zvcftoolz: a Python package for comparing and evaluating Variant Call Format files.accepted1.0.02018-11-27 13:36:06 UTC352019-03-26 06:29:14 UTC420191144SteveDavisU.S. Food and Drug Administration0000-0002-5581-192210.21105/joss.01144https://doi.org/10.5281/zenodo.2583998Pythonhttps://joss.theoj.org/papers/10.21105/joss.01144.pdfbioinformatics, next-generation sequencing, variant call format, VCFtag:joss.theoj.org,2005:Paper/1642017-03-18T00:00:00Z2021-02-15T11:34:13ZVCC: A framework for building containerized reproducible cluster software environmentsacceptedv1.02017-03-06 15:48:51 UTC112017-03-18 00:00:00 UTC22017208JoshuaHigginsHigh Performance Computing Research Group, University of Huddersfield0000-0003-1551-5552VioletaHolmesHigh Performance Computing Research Group, University of Huddersfield0000-0002-9786-4555ColinVentersHigh Performance Computing Research Group, University of Huddersfield10.21105/joss.00208https://doi.org/10.6084/m9.figshare.4763857JavaScripthttps://joss.theoj.org/papers/10.21105/joss.00208.pdfcontainers, HPC, reproducibility, virtualisation, clustertag:joss.theoj.org,2005:Paper/632016-10-25T00:00:00Z2021-02-15T11:34:25ZVCFPy: a Python 3 library with good support for both reading and writing VCFacceptedv0.7.02016-09-28 07:10:23 UTC62016-10-25 00:00:00 UTC1201685ManuelHoltgreweBerlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin0000-0002-3051-1763DieterBeuleBerlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin0000-0002-3284-063210.21105/joss.00085https://doi.org/10.6084/m9.figshare.3863583.v2Pythonhttps://joss.theoj.org/papers/10.21105/joss.00085.pdfVCF, software library