tag:joss.theoj.org,2005:/papers/tagged/sequencingJournal of Open Source Software2024-01-22T15:00:12ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48382024-01-22T15:00:12Z2024-01-23T11:55:19Zcstag and cstag-cli: tools for manipulating and visualizing cs tagsacceptedv1.0.42023-10-06 03:25:34 UTC932024-01-22 15:00:12 UTC920246066AkihiroKunoDepartment of Anatomy and Embryology, University of Tsukuba, Tsukuba, Ibaraki, Japan, Laboratory Animal Resource Center, Trans-border Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.0000-0002-4674-688210.21105/joss.06066https://doi.org/10.5281/zenodo.10544838Pythonhttps://joss.theoj.org/papers/10.21105/joss.06066.pdfpython, genomics, sequencing, bioinformaticstag:joss.theoj.org,2005:Paper/45402024-01-12T22:11:20Z2024-01-15T11:54:18Zcellanneal: A user-friendly deconvolution software for transcriptomics dataacceptedv1.0.02023-06-12 17:35:47 UTC932024-01-12 22:11:20 UTC920245610LisaBuchauerDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel, Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany0000-0002-4722-8390ShalevItzkovitzDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0003-0685-252210.21105/joss.05610https://doi.org/10.5281/zenodo.10405043Pythonhttps://joss.theoj.org/papers/10.21105/joss.05610.pdfbioinformatics, computational biology, mixture deconvolution, bulk deconvolution, transcriptomics, RNA sequencing, omics methodstag: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/42982023-10-19T10:05:08Z2023-10-20T00:00:55ZBaargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistanceacceptedv0.12023-03-10 09:09:20 UTC902023-10-19 10:05:08 UTC820235397JulietteHayerMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0003-4899-9637JacquesDainatMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France0000-0002-6629-0173EllaMarcyMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Centre Hospitalier Universitaire (CHU) Lapeyronie, Montpellier, France0009-0002-6000-1665Anne-LaureBañulsMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0002-2106-866710.21105/joss.05397https://doi.org/10.5281/zenodo.8386399Python, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.05397.pdfWhole Genome Shotgun, Genomics, Long reads sequencing technology, Short reads sequencing technology, Antimicrobial Resistance, Pangenometag:joss.theoj.org,2005:Paper/41882023-07-20T11:29:57Z2023-07-27T07:02:54ZSeqPanther: Sequence manipulation and mutation statistics toolsetacceptedv1.0.02023-02-03 07:59:06 UTC872023-07-20 11:29:57 UTC820235305JamesEmmanuelSanKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-5736-664XStephanievan WykCentre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2655-8518HouriiyahTegallyKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-7102-8540SimeonEcheYale University School of Medicine, New Haven, Connecticut, United States of America0000-0001-5494-8372EduanWilkinsonKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2503-9441AquillahM.KanziKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa0000-0001-6081-9438Tuliode OliveiraKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa, Department of Global Health, University of Washington, Seattle, WA, United States of America0000-0002-3027-5254AnmolM.KiranSchool of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland0000-0003-2680-230310.21105/joss.05305https://doi.org/10.5281/zenodo.8126922Pythonhttps://joss.theoj.org/papers/10.21105/joss.05305.pdfBioinformatics, sequence analysis, NGS, codon, amino acid substitution, nucleotide substitution, INDELtag:joss.theoj.org,2005:Paper/34432023-05-08T14:16:33Z2023-05-09T00:01:30ZsmmR: A Semi-Markov R packageaccepted1.0.2.92022-03-25 14:09:01 UTC852023-05-08 14:16:33 UTC820234365VladStefanBarbuLaboratory of Mathematics Raphaël Salem (LMRS), UMR CNRS 6085, University of Rouen Normandy, France0000-0002-0840-016XFlorianLecocqLaboratory of Mathematics Raphaël Salem (LMRS), UMR CNRS 6085, University of Rouen Normandy, FranceCorentinLothodéLaboratory of Mathematics Raphaël Salem (LMRS), UMR CNRS 6085, University of Rouen Normandy, France0000-0002-8209-317XNicolasVergneLaboratory of Mathematics Raphaël Salem (LMRS), UMR CNRS 6085, University of Rouen Normandy, France10.21105/joss.04365https://doi.org/10.5281/zenodo.7874883R, C++https://joss.theoj.org/papers/10.21105/joss.04365.pdfstatistics, Markov-chains, sequence, estimationtag:joss.theoj.org,2005:Paper/43552023-03-22T09:42:42Z2023-03-23T00:03:05ZPynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databasesacceptedv1.0.02023-03-20 17:14:26 UTC832023-03-22 09:42:42 UTC820235289SemidánRobaina-EstévezDepartment of Microbiology. University of La Laguna. Spain.0000-0003-0781-1677JoséM.GonzálezDepartment of Microbiology. University of La Laguna. Spain.0000-0002-9926-332310.21105/joss.05289https://doi.org/10.5281/zenodo.7750666Pythonhttps://joss.theoj.org/papers/10.21105/joss.05289.pdfbioinformatics, HMMER, synteny, HMMs, sequencingtag:joss.theoj.org,2005:Paper/37642022-11-04T21:27:26Z2022-11-08T13:57:28Zbtllib: A C++ library with Python interface for efficient genomic sequence processingacceptedv1.4.42022-08-04 01:28:45 UTC792022-11-04 21:27:26 UTC720224720VladimirNikolićCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada, Bioinformatics Graduate Program, The University of British Columbia, Vancouver, BC, Canada0000-0002-2992-9935ParhamKazemiCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada, Bioinformatics Graduate Program, The University of British Columbia, Vancouver, BC, CanadaLaurenCoombeCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada0000-0002-7518-2326JohnathanWongCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, CanadaAmirhosseinAfshinfardCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada, Bioinformatics Graduate Program, The University of British Columbia, Vancouver, BC, Canada0000-0002-6875-4939JustinChuCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada, Bioinformatics Graduate Program, The University of British Columbia, Vancouver, BC, CanadaRenéL.WarrenCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada0000-0002-9890-2293InançBirolCanada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada0000-0003-0950-783910.21105/joss.04720https://doi.org/10.5281/zenodo.7275416Python, C, Rhttps://joss.theoj.org/papers/10.21105/joss.04720.pdfC++, bioinformatics, algorithms, data structures, genome, bloom filtertag:joss.theoj.org,2005:Paper/32752022-10-08T07:54:59Z2022-10-10T12:31:52ZVPsearch: fast exact sequence similarity search for genomic sequencesaccepted0.2.02022-01-11 07:44:02 UTC782022-10-08 07:54:59 UTC720224236JorisVankerschaverCenter for Biosystems and Biotech Data Analysis, Ghent University Global Campus, Republic of Korea, Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium0000-0002-5813-5659StevenJ.KernEnthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States0000-0002-3789-7400RobertKernEnthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States10.21105/joss.04236https://doi.org/10.5281/zenodo.7142747Python, Cython, C++https://joss.theoj.org/papers/10.21105/joss.04236.pdfpython, genomics, bioinformaticstag:joss.theoj.org,2005:Paper/32532022-07-13T10:07:55Z2022-07-14T00:00:34ZMagphi: Sequence extraction tool from FASTA and GFF3 files using seed pairsacceptedv0.1.62021-12-17 00:01:19 UTC752022-07-13 10:07:55 UTC720224369MagnusG.JespersenDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-9751-9877AndrewHayesDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-8038-1656MarkR.DaviesDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia0000-0001-6141-517910.21105/joss.04369https://doi.org/10.5281/zenodo.6814768Pythonhttps://joss.theoj.org/papers/10.21105/joss.04369.pdfmicrobiology, genomics, genome