tag:joss.theoj.org,2005:/papers/tagged/quality%20controlJournal 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/23512022-01-08T15:59:42Z2022-01-09T00:01:14ZNanoq: ultra-fast quality control for nanopore readsacceptedv0.2.12021-01-24 00:25:52 UTC692022-01-08 15:59:42 UTC720222991EikeSteinigThe Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia0000-0001-5399-5353LachlanCoinThe Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia0000-0002-4300-455X10.21105/joss.02991https://doi.org/10.5281/zenodo.5816183Python, Rusthttps://joss.theoj.org/papers/10.21105/joss.02991.pdfont, nanopore, reads, filter, summary, statistics, length, qualitytag:joss.theoj.org,2005:Paper/30132021-11-30T18:19:17Z2021-12-01T00:02:35ZNextclade: clade assignment, mutation calling and quality control for viral genomesacceptedv1.3.02021-09-03 13:36:34 UTC672021-11-30 18:19:17 UTC620213773IvanAksamentovBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-7557-9673CorneliusRoemerBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-6138-6539EmmaB.HodcroftSwiss Institute of Bioinformatics, Basel, Switzerland, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland0000-0002-0078-2212RichardA.NeherBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0003-2525-140710.21105/joss.03773https://doi.org/10.5281/zenodo.5726681Ruby, C++https://joss.theoj.org/papers/10.21105/joss.03773.pdfphylogenetics, typing, sequence alignmenttag:joss.theoj.org,2005:Paper/14222020-04-07T18:41:34Z2021-02-15T11:31:12ZA Framework to Quality Control Oceanographic Dataaccepted0.21.02019-12-26 01:31:42 UTC482020-04-07 18:41:34 UTC520202063GuilhermeP.CastelaoScripps Institution of Oceanography0000-0002-6765-070810.21105/joss.02063https://doi.org/10.5281/zenodo.3733959Pythonhttps://joss.theoj.org/papers/10.21105/joss.02063.pdfoceanography, quality controltag:joss.theoj.org,2005:Paper/8462019-02-28T14:14:35Z2021-02-15T11:32:33ZpycoQC, interactive quality control for Oxford Nanopore Sequencingacceptedv2.2.02019-02-04 16:10:37 UTC342019-02-28 14:14:35 UTC420191236AdrienLegerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK0000-0001-8772-6776TommasoLeonardiGurdon Institute, Cambridge, Cambridgeshire, UK, Center for Genomic Science IIT\@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy0000-0002-4449-186310.21105/joss.01236https://doi.org/10.5281/zenodo.2578275Pythonhttps://joss.theoj.org/papers/10.21105/joss.01236.pdfpython3, plots, metrics, nanopore sequencing, interactive, quality controltag:joss.theoj.org,2005:Paper/4682018-05-17T10:17:56Z2021-02-15T11:33:27Zqicharts2: Quality Improvement Charts for Raccepted0.4.0.90002018-04-19 10:29:59 UTC252018-05-17 10:17:56 UTC32018699JacobAnhøjRigshospitalet, University of Copenhagen, Denmark0000-0002-7701-177410.21105/joss.00699https://doi.org/10.5281/zenodo.1244604Rhttps://joss.theoj.org/papers/10.21105/joss.00699.pdfStatistical process control, Continuous quality improvementtag: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/2012017-07-03T00:00:00Z2021-02-15T11:34:07Zkhmer release v2.1: software for biological sequence analysisacceptedv2.12017-05-26 00:17:17 UTC152017-07-03 00:00:00 UTC22017272DanielStandageLab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis0000-0003-0342-8531AliAliyariIntegrative Genetics and Genomics Graduate Group; University of California, Davis0000-0003-0925-4886LisaJ.CohenLab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis, Molecular, Cellular, and Integrative Physiology Graduate Group; University of California, Davis0000-0002-3600-7218MichaelR.CrusoeCommon Workflow Language Project0000-0002-2961-9670TimHeadWild Tree Tech0000-0003-0931-3698LuizIrberLab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis, Computer Science Graduate Group; University of California, Davis0000-0003-4371-9659ShannonEkJoslinIntegrative Genetics and Genomics Graduate Group; University of California, Davis0000-0001-5470-1193N.B.KingsleyIntegrative Genetics and Genomics Graduate Group; University of California, Davis0000-0001-8574-8592KevinD.MurrayARC Centre of Excellence in Plant Energy Biology; Australian National University0000-0002-2466-1917RussellNechesMicrobiology Graduate Group; Univerity of California, Davis0000-0002-2055-8381CamilleScottLab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis, Computer Science Graduate Group; University of California, Davis0000-0001-8822-8779RyanSheanUniversity of WashingtonSaschaSteinbissDebian Project0000-0002-2151-0574CaitSydneyGoogle, Inc.C.TitusBrownLab for Data Intensive Biology; School of Veterinary Medicine; University of California, Davis, Department of Population Health and Reproduction; School of Veterinary Medicine; University of California, Davis0000-0001-6001-267710.21105/joss.00272https://doi.org/10.5281/zenodo.822478Python, C++, Roffhttps://joss.theoj.org/papers/10.21105/joss.00272.pdfbioinformatics, sequence analysis, Bloom filter, Count-Min sketch, de Bruijn graph, assembly, graph traversal, streaming, quality controltag:joss.theoj.org,2005:Paper/1812017-05-26T00:00:00Z2021-02-15T11:34:11Zlibqcpp: A C++14 sequence quality control libraryaccepted0.4.02017-04-05 03:21:05 UTC132017-05-26 00:00:00 UTC22017232KevinD.MurrayARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT 2602, Australia0000-0002-2466-1917JustinO.BorevitzARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT 2602, Australia0000-0001-8408-369910.21105/joss.00232https://doi.org/10.5281/zenodo.583325C++, Chttps://joss.theoj.org/papers/10.21105/joss.00232.pdfnext-generation sequencing, c++, bioinformatics