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Evaluation of de novo assembly using PacBio long reads
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
2016 (English)Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
Abstract [en]

New sequencing technologies show promise for the construction of complete and accurate genome sequences, by a process called de novo assembly that joins reads by overlap to longer contiguous sequences without the need for a reference genome. High-quality de novo assembly leads to better understanding in genetic variations. The purpose of this thesis is to evaluate human genome sequences obtained from the PacBio sequencing platform, which is a new technology suitable for de novo assembly of large genomes. The evaluation focuses on comparing sequence identity between our own de novo assemblies and the available human reference and through that, benchmark accuracy of our data. Sequences that are absent from the reference genome, are investigated for potential unannotated genes coordinately. We also assess the complex structural variation using different approaches. Our assemblies show high consensus with the human reference genome, with ⇠ 98.6% of the bases in the assemblies mapped to the human reference. We also detect more than ten thousand of structural variants, including some large rearrangements, with respect to the reference.

Place, publisher, year, edition, pages
2016. , 21 p.
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:uu:diva-302744OAI: oai:DiVA.org:uu-302744DiVA: diva2:967428
Educational program
Master Programme in Bioinformatics
Presentation
2016-08-31, 14:00
Supervisors
Examiners
Available from: 2016-09-08 Created: 2016-09-08 Last updated: 2016-09-08Bibliographically approved

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Biology Education Centre
Bioinformatics (Computational Biology)

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