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ssvq [2018/04/13 08:06]
tischulz [Schedule] Presentation title added
ssvq [2018/04/13 08:08] (current)
tischulz [Talks] Title and abstract added
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 ==== Talks ==== ==== Talks ====
-**Title 1**+**Nanopore quasispezies reconstruction**
  
 //by Manja Marz// //by Manja Marz//
  
-Some text...+//​Introduction//:​ 
 +Third generation sequencing techniques have made it possible to generate read data of unprecedented length at a low cost. 
 +Relatively short sequenes such as viral genomes can now be fully covered by few or even singular long reads. 
 +Due to their error-prone replication mechanism, virus populations are made up of a diverse spectrum of haplotypes. Characterizing this so called quasispecies is an important task in virus discovery and diagnostics. 
 + 
 +//​Objectives//:​ 
 +We aim to demonstrate that long read sequencing of viral genomes allows fast identification and almost obsoletes assembly when single reads cover the whole genome. 
 +Furthermore,​ we aim to determine the viral haplotypes contained in a sample. 
 +Utilizing the long read information,​ it is possible to determine which specific sequence features (e.g. co-occuring SNPs, recombination events) occur in each haplotype. 
 + 
 +//​Methods//:​ 
 +Using the recently released Direct RNA kit for the Oxford Nanopore Technologies MinION platform we sequenced a human coronavirus 229E (HCoV-229E) sample from human cell culture. 
 +As a work-in-progress approach, a de Bruijn graph is constructed from the overlapping k-mers of the long read data while preserving the information denoting which k-mers originated from a single long read. 
 +After tip- and bulge removal, potential haplotype consensus sequences are produced by assembly of overlapping subgraph consensus sequences. 
 + 
 +//​Results//:​ 
 +Sequencing the coronavirus sample yielded 293k reads, of which 27% are of virus origin. Median read length was 2.5kb and two reads exceeded 26kb, thus covering almost the full HCoV-229E genome of 27.3kb. 
 +The de Bruijn graph reveals the haplotype subgraph structure, but subgraph separation and consensus generation is hindered by the high amount of sequencing errors of the platform (15% insertions and deletions). This could be rectified by an error correction step, but  
 +might indicate that other approaches prove more suitable. 
 + 
 +//​Conclusion//:​ 
 +Long read sequencing enables viral full genome sequencing with minimal assembly, and also captures haplotype information. 
 +However, sequencing errors disrupt haplotype separation and necessitate appropriate error correction steps.
  
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ssvq.txt · Last modified: 2018/04/13 08:08 by tischulz