The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact support@cyverse.org.


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 support@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
  4. Parameters
    1. Maximum number of reference genomes: Maximum number of reference genomes (per each assembly) to download after searching in SILVA database. Defaultvalue is 50.
    2. Ambiguity usage: Way of processing equally good alignments of a contig (probably repeats):

      noneskip all such alignments;
      onetake only one (the very best one);
      alluse all alignments. Can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.).



Test/sample data

The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/metaQUAST.sample.data

Test run

  1. Open MetaQUAST-4.0(denovo based) app in DE
  2. Select/drag input files (meta_contigs_1.fasta and meta_contigs_2.fasta) into the Inputs section of the app
  3. Select the name of the output file (metaQuast_output) in the output section of the app
  4. Ambiguity usage: all

Test Results

Successful execution of the QUAST assessment pipeline will create metaQuast_output folder

report.txtassessment summary in plain text format,
report.tsvtab-separated version of the summary, suitable for spreadsheets (Google Docs, Excel, etc),
report.texLaTeX version of the summary,
alignment.svgcontig alignment plot (file is created if matplotlib python library is installed),
report.pdfall other plots combined with all tables (file is created if matplotlib python library is installed),
report.htmlHTML version of the report with interactive plots inside,
contigs_reports/ 
misassemblies_reportdetailed report on misassemblies
unaligned_reportdetailed report on unaligned and partially unaligned contigs

 More detailed explanation of the above output is provided in metaQUAST manual

 

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