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HiLive: real-time mapping of illumina reads while sequencing
Martin S Lindner1, Benjamin Strauch1, Jakob M Schulze1
1Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.
Bioinformatics (Oxford, England)
|November 1, 2016
Summary
HiLive maps DNA sequencing reads in real time during sequencing, significantly reducing analysis time for clinical applications like precision medicine. This novel approach offers comparable accuracy to existing methods while accelerating results.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Next Generation Sequencing (NGS) is vital for clinical applications, but traditional read mapping is time-consuming.
- Current methods initiate read mapping only after sequencing completion and file conversion, creating bottlenecks.
Purpose of the Study:
- To introduce HiLive, a novel real-time read mapper designed to accelerate NGS data analysis.
- To reduce the overall sample analysis time in time-critical clinical settings.
Main Methods:
- HiLive employs a k-mer based alignment strategy to process data in real time.
- It continuously reads intermediate BCL files from Illumina sequencers, extending alignments as new data becomes available.
Main Results:
- HiLive reported final read alignments within minutes after a full Illumina HiSeq 1500 run.
- FASTQ file conversion alone took approximately five times longer than HiLive's complete analysis.
- HiLive demonstrated comparable accuracy to existing read mappers on simulated and real data.
Conclusions:
- HiLive drastically reduces sample analysis time in clinical NGS applications.
- The real-time mapping capability of HiLive is crucial for time-sensitive fields like precision medicine.
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