tag:joss.theoj.org,2005:/papers/tagged/long%20read%20sequencingJournal of Open Source Software2023-10-19T10:05:08ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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-LaureBaƱulsMIVEGEC, 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/13402019-12-11T23:26:26Z2021-02-15T11:31:21Zalignparse: A Python package for parsing complex features from high-throughput long-read sequencingaccepted0.1.02019-11-19 23:52:10 UTC442019-12-11 23:26:26 UTC420191915KatharineH.d.CrawfordBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, Washington, USA0000-0002-6223-4019JesseD.BloomBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Howard Hughes Medical Institute, Seattle, Washington, USA0000-0003-1267-340810.21105/joss.01915https://doi.org/10.5281/zenodo.3569587Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.01915.pdfPacBio, deep mutational scanning, single-cell virus sequencing, genomics, sequencingtag:joss.theoj.org,2005:Paper/9092019-04-04T03:07:41Z2021-02-15T11:32:28ZBadread: simulation of error-prone long readsacceptedv0.1.32019-03-01 11:22:17 UTC362019-04-04 03:07:41 UTC420191316RyanR.WickDepartment of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia0000-0001-8349-077810.21105/joss.01316https://doi.org/10.5281/zenodo.2622997Pythonhttps://joss.theoj.org/papers/10.21105/joss.01316.pdflong-read sequencing, oxford nanopore, ont, pacific biosciences, pacbiotag:joss.theoj.org,2005:Paper/6582019-03-01T14:33:49Z2021-02-15T11:32:54ZTipToft: detecting plasmids contained in uncorrected long read sequencing dataacceptedv0.1.42018-10-09 10:49:56 UTC352019-03-01 14:33:49 UTC420191021AndrewJ.PageQuadram Institute Bioscience, Norwich Research Park, Norwich, UK.0000-0001-6919-6062TorstenSeemannMelbourne Bioinformatics, The University of Melbourne, Parkville, Australia.0000-0001-6046-610X10.21105/joss.01021https://doi.org/10.5281/zenodo.2561192Pythonhttps://joss.theoj.org/papers/10.21105/joss.01021.pdfbioinformatics, plasmid typing, long read sequencing, bacteria