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Quast Specifications

Process Details

  • Name: Quast
  • Process UUID: sojkaae9m4tdp7tz1og2rpq89y9qkn
  • Process Group: Assembly

Overview

Quast (Quality Assessment Tool for Genome Assemblies) is a comprehensive genome assembly evaluation tool that provides detailed quality metrics and statistics for genome assemblies. This process analyzes FASTA files containing assembled genomes and generates comprehensive reports on assembly quality, including metrics such as N50, contig statistics, and assembly completeness measures.

This process is implemented in Bash within a Nextflow workflow framework, utilizing the containerized Quast v5.2.0 tool.

Key Functionality

  • Assembly Quality Assessment: Evaluates genome assemblies using standard quality metrics including N50, L50, total length, and contig distribution
  • Statistical Analysis: Generates comprehensive statistics on contig sizes, assembly fragmentation, and overall assembly quality
  • Multi-threaded Processing: Utilizes available CPU cores for efficient processing of large genome assemblies
  • Standardized Reporting: Produces standardized TSV output files for downstream analysis and comparison

Input/Output Specification

Inputs

Required Inputs

  • FASTA File
    • Description: Genome assembly file containing contigs or scaffolds to be evaluated
    • Format: FASTA format

Outputs

  • Log File

    • Description: Process execution log containing runtime information and any error messages
    • Format: LOG format

  • Output Directory

    • Description: Complete directory containing all Quast analysis results and intermediate files
    • Format: Directory structure

  • Transposed Report TSV

    • Description: Tab-separated values file containing transposed assembly quality metrics and statistics
    • Format: TSV format

Parameters & Settings

This process uses default Quast parameters optimized for genome assembly evaluation. No user-configurable parameters are available through the Foundry UI for this process.

References & Resources

  • Tool Documentation: Contact the team for details on the Quast implementation
  • Related Papers: Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072-1075. https://doi.org/10.1093/bioinformatics/btt086