tag:joss.theoj.org,2005:/papers/tagged/sketchJournal of Open Source Software2019-12-10T18:30:45ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/12262019-12-10T18:30:45Z2021-02-15T11:31:35ZMashtree: a rapid comparison of whole genome sequence filesacceptedv0.572019-09-18 20:34:06 UTC442019-12-10 18:30:45 UTC420191762LeeS.KatzEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA, Center for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-2533-9161TaylorGriswoldEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USAShataviaS.MorrisonRespiratory Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0002-4658-5951JasonA.CaravasRespiratory Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0001-9111-406XShaokangZhangCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0003-0874-2212HenkC. denBakkerCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-4086-1580XiangyuDengCenter for Food Safety, University of Georgia, Griffin, GA, USAHeatherA.CarletonEnteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA10.21105/joss.01762https://doi.org/10.5281/zenodo.3568386Perlhttps://joss.theoj.org/papers/10.21105/joss.01762.pdfdendrogram, mash, sketch, tree, rapidtag: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/172016-09-14T00:00:00Z2021-02-15T11:34:33Zsourmash: a library for MinHash sketching of DNAaccepted0.9.22016-06-11 19:41:26 UTC52016-09-14 00:00:00 UTC1201627C.TitusBrownUniversity of California, Davis0000-0001-6001-2677LuizIrberUniversity of California, Davis0000-0003-4371-965910.21105/joss.00027https://doi.org/10.5281/zenodo.153989Rust, Python, C++https://joss.theoj.org/papers/10.21105/joss.00027.pdfMinHash, k-mers