MetaQUAST-4.0 (reference based) in DE

Owned by upendra kumar Devisetty
Last updated: Jun 15, 2017
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The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to upendra@cyverse.org. Thank you.

Rationale and background:

QUAST: QUality ASsesment Tool for Genome Assemblies. MetaQUAST is the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools

Gurevich, A., Saveliev, V., Vyahhi, N., and Tesler, G. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075

QUAST is a tool for evaluating genome assemblies by computing various metrics, including 

  • N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length,
  • NG50, where length of the reference genome is being covered,
  • NA50 and NGA50, where aligned blocks instead of contigs are taken,
  • misassemblies, misassembled and unaligned contigs or contigs bases,
  • genes and operons covered

QUAST Builds convenient plots for different metrics

  • cumulative contigs length,
  • all kinds of N-metrics,
  • genes and operons covered,
  • GC content.

Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Input file(s)
    1. Input file (Genome assemblies generated by using any of the genome assemblers in fasta format)
  3. Output
    1. Output directory name
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