Blog
About

3
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

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

      Preprint

      ,

      bioRxiv

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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. 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.

          Findings

          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 the most common alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies. We found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.

          Related collections

          Author and article information

          Journal
          bioRxiv
          June 06 2019
          Article
          10.1101/663401
          © 2019
          Product

          Quantitative & Systems biology, Biophysics

          Comments

          Comment on this article