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.
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.
Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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Evidence ID | Analyze ID | File | Description |
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