{"data":{"id":"10.6084/m9.figshare.712587","type":"dois","attributes":{"doi":"10.6084/m9.figshare.712587","prefix":"10.6084","suffix":"m9.figshare.712587","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Chin, Jason","nameType":"Personal","givenName":"Jason","familyName":"Chin","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[],"dates":[{"date":"2013-06-06","dateType":"Created"},{"date":"2015-12-02","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["486406546 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This fileset contains data, code and IPython Notebooks demostrating\u003cbr\u003ehow to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through\u003cbr\u003e''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to \"gunzip\" the two main data file ''preads.fa.gz'' and\u003cbr\u003e''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''\u003cbr\u003ecan be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''\u003cbr\u003eand ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the\u003cbr\u003ecomputational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''. Thanks Carsten Russ (Broad Institute) and Sarah Volkmann (Harvard School of Public Health) for providing the DNA sample.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Plasmodium_3D7_Genome_Assembly_With_PacBio_Data_and_CLEAR_/712587","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2013-06-06T18:35:46.000Z","registered":"2013-06-06T18:35:48.000Z","published":"2013","updated":"2020-09-05T01:54:39.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.712587","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}