A combined de novo assembly approach increases the quality of prokaryotic draft genomes

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dc.authorid0000-0002-4443-3065en_US
dc.authorid0000-0003-0097-1125en_US
dc.contributor.authorÇabuk, Uğur
dc.contributor.authorÜnlü, Ercan Selçuk
dc.date.accessioned2023-08-04T06:46:20Z
dc.date.available2023-08-04T06:46:20Z
dc.date.issued2022en_US
dc.departmentBAİBÜ, Lisansüstü Eğitim Enstitüsü, Fen Bilimleri, Biyoloji Ana Bilim Dalıen_US
dc.description.abstractNext-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.en_US
dc.identifier.citationÇabuk, U., & Ünlü, E. S. (2022). A combined de novo assembly approach increases the quality of prokaryotic draft genomes. Folia Microbiologica, 67(5), 801-810.en_US
dc.identifier.doi10.1007/s12223-022-00980-7
dc.identifier.endpage810en_US
dc.identifier.issn0015-5632
dc.identifier.issn1874-9356
dc.identifier.issue5en_US
dc.identifier.pmid35668290en_US
dc.identifier.scopus2-s2.0-85131411394en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.startpage801en_US
dc.identifier.urihttp://dx.doi.org/10.1007/s12223-022-00980-7
dc.identifier.urihttps://hdl.handle.net/20.500.12491/11428
dc.identifier.volume67en_US
dc.identifier.wosWOS:000806656300001en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorÇabuk, Uğur
dc.institutionauthorÜnlü, Ercan Selçuk
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.ispartofFolia Microbiologicaen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - İdari Personel ve Öğrencien_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectDe Novo Assemblyen_US
dc.subjectProkaryotesen_US
dc.subjectBacteriaen_US
dc.subjectSingle-Cellen_US
dc.subjectSequenceen_US
dc.subjectToolen_US
dc.titleA combined de novo assembly approach increases the quality of prokaryotic draft genomesen_US
dc.typeArticleen_US

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