Abstract
BackgroundNext-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.ResultsThis 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.ConclusionsCompared 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.
Highlights
Next-generation sequencing (NGS) technologies has brought an unprecedented amount of genomic data for analysis
This study proposes an efficient visualization pipeline for NGS data and implements a lightweight read coverage viewer, Light-RCV, with the proposed pipeline
This study proposed four designs on visualizing read counts of each genomic position
Summary
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, singlenucleotide polymorphism (SNP), novel transcript discovery, etc. Instead of reporting a single expression value for each transcript in array-based profiling technologies, NGS technologies can reveal the read count variation within a transcript at the base level Such a base-level read coverage provides further insights for analyzing alternative mRNA splicing, single-nucleotide polymorphism (SNP), novel transcript discovery, etc [3,4]. Many NGS viewers, such as Artemis [5], Savant [6], Tablet [7] and Integrative Genomics Viewer (IGV) [8], have been developed to visualize read alignments into friendly graphic profiles Some of these NGS viewers can depict a base-level read coverage but only in a small scale; while some of them provide a genome-wide read coverage but not at the base level. The considerable data scale and computational complexity pose a challenge to develop such tools
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