tag:joss.theoj.org,2005:/papers/tagged/genome%20assemblyJournal of Open Source Software2020-10-12T19:51:22ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/18302020-10-12T19:51:22Z2021-02-15T11:30:20ZCPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assembliesacceptedv2.1.02020-07-06 08:33:06 UTC542020-10-12 19:51:22 UTC520202473PrakkiSai RamaSridattaNational Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore0000-0002-9254-2557NataschaM.ThevasagayamNational Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, SingaporeWeizhenXuNational Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, SingaporeKalisvarMarimuthuNational Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, SingaporeJeanetteW pTeoNational University Hospital, SingaporeIndumathiVenkatachalamSingapore General Hospital, SingaporeNgOonTekNational Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore10.21105/joss.02473https://doi.org/10.5281/zenodo.4076089Rhttps://joss.theoj.org/papers/10.21105/joss.02473.pdfCarbapenamase gene profile, cocarriage, Beta-lactamases, Antimicrobial resistance (AMR)tag:joss.theoj.org,2005:Paper/6372019-01-22T19:10:25Z2021-02-15T11:32:57ZGFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formatsacceptedv1.0.02018-09-24 10:52:02 UTC332019-01-22 19:10:25 UTC420191083EricT.DawsonDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA, Department of Genetics, University of Cambridge, Cambridge, UK, Wellcome Sanger Institute, Hinxton, UK0000-0001-5448-1653RichardDurbinDepartment of Genetics, University of Cambridge, Cambridge, UK, Wellcome Sanger Institute, Hinxton, UK0000-0002-9130-100610.21105/joss.01083https://doi.org/10.5281/zenodo.2546721Perl, C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.01083.pdfGFA, genome assembly, bioinformaticstag:joss.theoj.org,2005:Paper/3422018-02-08T11:29:57Z2021-02-15T11:33:44Zreper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genomeacceptedv1.0.02017-12-21 17:14:53 UTC222018-02-08 11:29:57 UTC32018527NiklasTerhoevenCenter for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität Würzburg0000-0002-8669-0000JörgSchultzCenter for Computational and Thoeretical Biology, Universität Würzburg, Lehrstuhl für Bioinformatik, Universität WürzburgThomasHacklDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology0000-0002-0022-320X10.21105/joss.00527https://doi.org/10.5281/zenodo.1167969Perl, Rhttps://joss.theoj.org/papers/10.21105/joss.00527.pdfrepeats, transposons, kmer, pipeline, repeat landscape, NGStag:joss.theoj.org,2005:Paper/2882018-01-16T12:42:02Z2021-02-15T11:33:52ZchloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun dataacceptedv1.0.02017-09-29 05:50:43 UTC212018-01-16 12:42:02 UTC32018464MarkusJ.AnkenbrandDepartment of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Germany, These authors contributed equally to this work0000-0002-6620-807XSimonPfaffCenter for Computational and Theoretical Biology, University of Würzburg, These authors contributed equally to this work0000-0001-8505-9439NiklasTerhoevenCenter for Computational and Theoretical Biology, University of Würzburg, Department of Bioinformatics, University of WürzburgMusgaQureischiDepartment of Bioinformatics, University of Würzburg, Centre for Experimental Molecular Medicine, University Clinics Würzburg, Germany0000-0001-9661-8494MaikGündelDepartment of Bioinformatics, University of Würzburg0000-0002-0502-4576ClemensL.WeißResearch Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, GermanyThomasHacklDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology0000-0002-0022-320XFrankFörsterCenter for Computational and Theoretical Biology, University of Würzburg, Department of Bioinformatics, University of Würzburg, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Applied Ecology and Bioresources, Gießen, Germany0000-0003-4166-542310.21105/joss.00464https://doi.org/10.5281/zenodo.1148955R, Perlhttps://joss.theoj.org/papers/10.21105/joss.00464.pdfchloroplast, genome, assemblytag:joss.theoj.org,2005:Paper/2022017-07-13T00:00:00Z2021-02-15T11:34:06ZKindel: indel-aware consensus for nucleotide sequence alignmentsacceptedv0.2.02017-05-26 11:32:21 UTC152017-07-13 00:00:00 UTC22017282BedeConstantinidesEvolution and Genomic Sciences, University of Manchester, Manchester, UK0000-0002-3480-3819DavidL.RobertsonMRC-University of Glasgow Centre for Virus Research, Glasgow, UK0000-0001-6338-022110.21105/joss.00282https://doi.org/10.5281/zenodo.826723Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.00282.pdfbioinformatics, sequence analysis, genome assemblytag:joss.theoj.org,2005:Paper/1152016-11-17T00:00:00Z2022-11-03T17:10:09ZRAILS and Cobbler: Scaffolding and automated finishing of draft genomes using long DNA sequencesacceptedv1.12016-11-11 00:02:49 UTC72016-11-17 00:00:00 UTC12016116ReneL.WarrenBC Cancer Agency, Genome Sciences Centre, Vancouver, BC, Canada0000-0002-9890-229310.21105/joss.00116https://doi.org/10.5281/zenodo.167092Perlhttps://joss.theoj.org/papers/10.21105/joss.00116.pdfDe novo sequence assembly, Genome scaffolding, Automated genome finishing, LINKS, RAILS