title: HiLive: real-time mapping of illumina reads while sequencing.
abstract: Next Generation Sequencing is increasingly used in time critical, clinical applications. While read mapping algorithms have always been optimized for speed, they follow a sequential paradigm and only start after finishing of the sequencing run and conversion of files. Since Illumina machines write intermediate output results, HiLive performs read mapping while still sequencing and thereby drastically reduces crucial overall sample analysis time, e.g. in precision medicine.
  
  
  
  We present HiLive as a novel real time read mapper that implements a k-mer based alignment strategy. HiLive continuously reads intermediate BCL files produced by Illumina sequencers and then extends initial k-mer matches by increasingly produced data from the sequencer.
  
  
  
  We applied HiLive on real human transcriptome data to show that final read alignments are reported within few minutes after the end of a full Illumina HiSeq 1500 run, while already the necessary conversion to FASTQ files as the standard input to current read mapping methods takes roughly five times as long. Further, we show on simulated and real data that HiLive has comparable accuracy to recent read mappers.
  
  
  
  HiLive and its source code are freely available from https://gitlab.com/SimonHTausch/HiLive .
  
  
  
  renardB@rki.de.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.
authors: Martin S
authors: MS
authors: Lindner
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.
authors: Benjamin
authors: B
authors: Strauch
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.
authors: Jakob M
authors: JM
authors: Schulze
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.|Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany.
authors: Simon H
authors: SH
authors: Tausch
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.|Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany.
authors: Piotr W
authors: PW
authors: Dabrowski
authors: Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany.
authors: Andreas
authors: A
authors: Nitsche
authors: Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany.
authors: Bernhard Y
authors: BY
authors: Renard
mesh_terms: D000465:Algorithms; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome