/
MetaQUAST-4.3 (denovo based) in DE

MetaQUAST-4.3 (denovo based) in DE

Jun 15, 2017



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

  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):




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-4.3(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. Maximum number of reference genomes: 50

  5. Ambiguity usage: all

Test Results

Successful execution of the QUAST assessment pipeline will create metaQuast_output folder

report.txt

assessment summary in plain text format,

report.tsv

tab-separated version of the summary, suitable for spreadsheets (Google Docs, Excel, etc),

report.tex

LaTeX version of the summary,

alignment.svg

contig alignment plot (file is created if matplotlib python library is installed),

report.pdf

all other plots combined with all tables (file is created if matplotlib python library is installed),

report.html

HTML version of the report with interactive plots inside,

contigs_reports/

 

misassemblies_report

detailed report on misassemblies

unaligned_report

detailed report on unaligned and partially unaligned contigs



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