title: Light-RCV: a lightweight read coverage viewer for next generation sequencing data.
abstract: BACKGROUND
  Next-generation sequencing (NGS) technologies has brought an unprecedented amount of genomic data for analysis. Unlike array-based profiling technologies, NGS can reveal the expression profile across a transcript at the base level. Such a base-level read coverage provides further insights for alternative mRNA splicing, single-nucleotide polymorphism (SNP), novel transcript discovery, etc. However, to our best knowledge, none of existing NGS viewers can timely visualize genome-wide base-level read coverages in an interactive environment.
  
  
  RESULTS
  This study proposes an efficient visualization pipeline and implements a lightweight read coverage viewer, Light-RCV, with the proposed pipeline. Light-RCV consists of four featured designs on the path from raw NGS data to the final visualized read coverage: i) read coverage construction algorithm, ii) multi-resolution profiles, iii) two-stage architecture and iv) storage format. With these designs, Light-RCV achieves a < 0.5s response time on any scale of genomic ranges, including whole chromosomes. Finally, a case study was performed to demonstrate the importance of visualizing base-level read coverage and the value of Light-RCV.
  
  
  CONCLUSIONS
  Compared with multi-functional genome viewers such as Artemis, Savant, Tablet and Integrative Genomics Viewer (IGV), Light-RCV is designed only for visualization. Therefore, it does not provide advanced analyses. However, its backend technology provides an efficient kernel of base-level visualization that can be easily embedded to other viewers. This viewer is the first to provide timely visualization of genome-wide read coverage at the base level in an interactive environment. The software is available for free at http://lightrcv.ee.ncku.edu.tw.
authors.forename: Che-Wei
authors.initials: CW
authors.lastname: Chang
authors.forename: Wen-Bin
authors.initials: WB
authors.lastname: Lee
authors.forename: An
authors.initials: A
authors.lastname: Chen-Deng
authors.forename: Tsunglin
authors.initials: T
authors.lastname: Liu
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Tseng
authors.forename: Darby Tien-Hao
authors.initials: DT
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D016681:Genome, Fungal; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface