4.6 Article

Alvis: a tool for contig and read ALignment VISualisation and chimera detection

Journal

BMC BIOINFORMATICS
Volume 22, Issue 1, Pages -

Publisher

BMC
DOI: 10.1186/s12859-021-04056-0

Keywords

Sequence alignment; Genomics; Visualisation; Chimera detection

Funding

  1. BBSRC Core Strategic Programme Grant [BB/CSP17270/1]

Ask authors/readers for more resources

Alvis is a simple command line tool that generates visualizations for various alignment analysis tasks, improving understanding of assembly quality and identifying potential errors. Splitting chimeric reads using Alvis output can enhance assembly contiguity while maintaining correctness.
Background The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others. Results We developed Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies. Conclusion Alvis diagrams facilitate improved understanding of assembly quality, enable read coverage to be visualised and potential errors to be identified. Additionally, we found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available