tag:joss.theoj.org,2005:/papers/reviewed_by/@telatinJournal of Open Source Software2024-02-27T21:44:24ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/49062024-02-12T12:06:13Z2024-02-13T00:01:22ZFasten: a toolkit for streaming operations on fastq filesacceptedv0.7.22023-10-30 19:01:17 UTC942024-02-12 12:06:13 UTC920246030LeeS.KatzEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, United States of America, Center for Food Safety, University of Georgia, Griffin, GA, United States of America0000-0002-2533-9161JohnPhanGeneral Dynamics Information Technology Inc., Atlanta, GA, United States of America0000-0002-4670-2660HenkC. denBakkerEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, United States of America0000-0002-4086-158010.21105/joss.06030https://doi.org/10.5281/zenodo.10621531Rusthttps://joss.theoj.org/papers/10.21105/joss.06030.pdfcommand line, fastq manipulation, interleaved fastqtag:joss.theoj.org,2005:Paper/31102021-12-24T16:41:35Z2021-12-25T00:01:13ZSepia, a taxonomy oriented read classifier in Rustacceptedv0.0.22021-10-14 16:38:44 UTC682021-12-24 16:41:35 UTC620213839HenkC. denBakkerCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-4086-1580LeeS.KatzCenter for Food Safety, University of Georgia, Griffin, GA, USA, Enteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0002-2533-916110.21105/joss.03839https://doi.org/10.5281/zenodo.5787248Python, Rusthttps://joss.theoj.org/papers/10.21105/joss.03839.pdfread classification, taxonomytag:joss.theoj.org,2005:Paper/18112020-09-23T23:57:46Z2022-01-18T11:38:56ZChromatiblock: scalable whole-genome visualization of structural differences in prokaryotesacceptedv0.4.22020-07-01 04:17:07 UTC532020-09-23 23:57:46 UTC520202451MitchellJohnSullivanDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of AmericaHarmvan BakelDepartment of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America10.21105/joss.02451https://doi.org/10.5281/zenodo.4034604Pythonhttps://joss.theoj.org/papers/10.21105/joss.02451.pdfBioinformatics, Microbial genomics, Visualization, multiple alignment