Abstract：
:The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby, our new algorithm allows for accurate read mapping results for intermediate cycles and supports large reference genomes such as the complete human reference. This enables the combination of real-time read mapping results with complex follow-up analysis. In this study, we showed the accuracy and scalability of our approach by applying real-time read mapping and variant calling to seven publicly available human whole exome sequencing datasets. Thereby, up to 89% of all detected SNPs were already identified after 40 sequencing cycles while showing similar precision as at the end of sequencing. Final results showed similar accuracy to those of conventional post-hoc analysis methods. When compared to standard routines, our live approach enables considerably faster interventions in clinical applications and infectious disease outbreaks. Besides variant calling, our approach can be adapted for a plethora of other mapping-based analyses.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Loka TP,Tausch SH,Renard BYdoi
10.1038/s41598-019-52991-zsubject
Has Abstractpub_date
2019-11-11 00:00:00pages
16502issue
1issn
2045-2322pii
10.1038/s41598-019-52991-zjournal_volume
9pub_type
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