tag:joss.theoj.org,2005:/papers/tagged/sequencing?page=2Journal of Open Source Software2022-05-07T21:21:13ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/30062022-05-07T21:21:13Z2022-05-08T00:01:23ZROCK: digital normalization of whole genome sequencing dataacceptedv_1.9.42021-09-01 12:54:20 UTC732022-05-07 21:21:13 UTC720223790VéroniqueNbspLegrandInstitut Pasteur, Université Paris Cité, Plateforme HPC, F-75015 Paris, FranceThomasNbspKergrohenPrédicteurs moléculaires et nouvelles cibles en oncologie, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France, Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, FranceNicolasNbspJolyInstitut Pasteur, Université Paris Cité, Plateforme HPC, F-75015 Paris, FranceAlexisNbspCriscuoloInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France, Institut Pasteur, Université Paris Cité, Plateforme de Microbiologie Mutualisée (P2M), F-75015 Paris, France0000-0002-8212-521510.21105/joss.03790https://doi.org/10.5281/zenodo.6527091M4, C++https://joss.theoj.org/papers/10.21105/joss.03790.pdfhigh-throughput sequencing, digital normalization, _k_-mertag:joss.theoj.org,2005:Paper/32002022-03-22T13:06:50Z2022-03-23T00:00:48Zhelayo: Reconstructing Sanskrit texts from manuscript witnessesacceptedv0.5 (helayo) v0.8 (matrix editor)2021-12-01 14:16:58 UTC712022-03-22 13:06:50 UTC720224022CharlesLiCentre nationale de la recherche scientifique, École des hautes études en sciences sociales0000-0001-8247-937410.21105/joss.04022https://doi.org/10.5281/zenodo.6334073Haskell, JavaScript, XSLThttps://joss.theoj.org/papers/10.21105/joss.04022.pdfJavascript, critical editing, philology, Sanskrit, sequence alignmenttag:joss.theoj.org,2005:Paper/31122022-01-29T00:57:26Z2022-01-30T00:01:13ZRasusa: Randomly subsample sequencing reads to a specified coverageaccepted0.6.02021-10-18 02:52:22 UTC692022-01-29 00:57:26 UTC720223941MichaelB.HallEuropean Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK0000-0003-3683-620810.21105/joss.03941https://doi.org/10.5281/zenodo.5895111Rusthttps://joss.theoj.org/papers/10.21105/joss.03941.pdfbioinformatics, genomics, fastq, fasta, subsampling, randomtag:joss.theoj.org,2005:Paper/29732022-01-29T00:44:59Z2022-01-30T00:01:17ZBam-readcount - rapid generation of basepair-resolution sequence metricsaccepted1.02021-08-15 14:11:57 UTC692022-01-29 00:44:59 UTC720223722AjayKhannaDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MODavidE.LarsonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Benson Hill, Inc. St. Louis, MOSridharNonavinkereSrivatsanDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MOMatthewMosiorDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Moffitt Cancer Center, Tampa, FLTravisE.AbbottMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Google, Inc. Mountain View, CASusannaKiwalaMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOTimothyJ.LeyDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOEricJ.DuncavageDepartment of Pathology, Washington University School of Medicine, St. Louis, MOMatthewJ.WalterDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOJasonR.WalkerMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOObiL.GriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOMalachiGriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOChristopherA.MillerDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO10.21105/joss.03722https://doi.org/10.5281/zenodo.5879149Rhttps://joss.theoj.org/papers/10.21105/joss.03722.pdfgenomics, cpp, sequencingtag:joss.theoj.org,2005:Paper/30132021-11-30T18:19:17Z2021-12-01T00:02:35ZNextclade: clade assignment, mutation calling and quality control for viral genomesacceptedv1.3.02021-09-03 13:36:34 UTC672021-11-30 18:19:17 UTC620213773IvanAksamentovBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-7557-9673CorneliusRoemerBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0002-6138-6539EmmaB.HodcroftSwiss Institute of Bioinformatics, Basel, Switzerland, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland0000-0002-0078-2212RichardA.NeherBiozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0003-2525-140710.21105/joss.03773https://doi.org/10.5281/zenodo.5726681Ruby, C++https://joss.theoj.org/papers/10.21105/joss.03773.pdfphylogenetics, typing, sequence alignmenttag:joss.theoj.org,2005:Paper/18072021-05-04T14:15:21Z2021-05-05T00:02:35Zstarfish: scalable pipelines for image-based transcriptomicsacceptedv0.2.12020-06-29 18:47:44 UTC612021-05-04 14:15:21 UTC620212440ShannonAxelrodChan Zuckerberg InitiativeMatthewCaiChan Zuckerberg Initiative0000-0003-4998-6328AmbroseJ.CarrChan Zuckerberg Initiative0000-0002-8457-2836JeremyFreemanChan Zuckerberg Initiative0000-0001-7077-7972DeepGanguliChan Zuckerberg InitiativeJustinT.KigginsChan Zuckerberg Initiative0000-0002-4638-7015BrianLongAllen Institute for Brain Science0000-0002-7793-5969TonyTungChan Zuckerberg InitiativeKevinA.YamauchiChan Zuckerberg Biohub0000-0002-7818-138810.21105/joss.02440https://doi.org/10.5281/zenodo.4734993Jupyter Notebook, Python, wdlhttps://joss.theoj.org/papers/10.21105/joss.02440.pdfxarray, skimage, microscopy, imaging, biology, single cell biology, spatial transcriptomics, MERFISH, In Situ Sequencing, osmFISH, smFISH, BaristaSeq, dartfish, starmap, seqFISHtag:joss.theoj.org,2005:Paper/21592021-01-23T22:18:17Z2021-02-15T11:29:43ZParent-map: analysis of parental contributions to evolved or engineered protein or DNA sequencesaccepted1.1.02020-11-18 06:55:03 UTC572021-01-23 22:18:17 UTC620212864DamienMarsicPorton Biologics, 388 Xinping Street, Suzhou Industrial Park, Jiangsu 215021, China0000-0003-0847-809510.21105/joss.02864https://doi.org/10.5281/zenodo.4459006Pythonhttps://joss.theoj.org/papers/10.21105/joss.02864.pdfDirected evolution, AAV, Sequence analysistag:joss.theoj.org,2005:Paper/14392020-04-26T12:39:35Z2021-02-15T11:31:09ZscTree: An R package to generate antibody-compatible classifiers from single-cell sequencing dataaccepted0.0.52020-01-14 14:41:38 UTC482020-04-26 12:39:35 UTC520202061J.SebastianPaezPurdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology0000-0002-0065-1474MichaelK.WendtPurdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology0000-0002-3665-7413NadiaAtallahLanmanPurdue University, Center for Cancer Research, Purdue University, Department of Comparative Pathobiology0000-0002-1819-707010.21105/joss.02061https://doi.org/10.5281/zenodo.3766467Rhttps://joss.theoj.org/papers/10.21105/joss.02061.pdfBioinformatics, Single cell, Flow Cytometrytag:joss.theoj.org,2005:Paper/14612020-03-06T17:24:08Z2021-02-15T11:31:05Zcovtobed: a simple and fast tool to extract coverage tracks from BAM filesacceptedv1.0.02020-01-30 15:43:55 UTC472020-03-06 17:24:08 UTC520202119GiovanniBiroloDept. Medical Sciences, University of Turin, ITALYAndreaTelatinGut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, UK0000-0001-7619-281X10.21105/joss.02119https://doi.org/10.5281/zenodo.3695204C++https://joss.theoj.org/papers/10.21105/joss.02119.pdfbedtools, bamtools, genomics, bioinformatics, target enrichment, sequence coveragetag:joss.theoj.org,2005:Paper/14652020-03-01T23:11:55Z2021-02-15T11:31:03Zfqfa: A pure Python package for genomic sequence filesacceptedv0.0.22020-02-03 22:59:17 UTC472020-03-01 23:11:55 UTC520202076AlanF.RubinThe Walter and Eliza Hall Institute of Medical Research, The University of Melbourne0000-0003-1474-605X10.21105/joss.02076https://doi.org/10.5281/zenodo.3688838Pythonhttps://joss.theoj.org/papers/10.21105/joss.02076.pdfgenomics, bioinformatics