Overview

metagenomix allows creating command-lines to run shotgun metagenomics analysis softwares one after another according to pipelines and parameters (for the softwares and for HPC computing resources) that can be fully configured by the user, including sample groups for co-assembly as well as species to target for strain-level analyses. Beside the main purpose of creating pipelines, metagenomix allows monitoring, managing and exporting the outputs of these pipelines.

Contents

Please explore the documentation before using:

• Usage
  • Creating
    • Input
      • Fastq file folders
      • Sample names
      • Sample merging
    • Output
      • Jobs
      • Terminal output
      • Runs output
      • Running jobs
    • Computing and monitoring
      • Computing
      • Monitoring and behaviour
    • Job chunks
    • Force re-writing
    • Usage
  • Managing
    • Rationale
    • Inputs
    • Management tasks
      • 1. Storage
        • Interaction
        • Output
      • 2. Jobs cleansing
        • Interaction
        • Output
      • 3. Renaming
        • Interaction
        • Output
    • Usage
  • Monitoring
  • Exporting
    • Input
      • Softwares
      • Extensions and regular expressions
    • Output
      • Archive
      • Terminal display
    • Usage
  • Merging
• Configuration
  • metadata
  • pipeline
  • databases
  • parameters
  • modules
  • co-assembly
  • strains
• Softwares
  • Sequence filtering
  • Pre-processing
  • Ecological distance measure
  • Paired-read merging
  • Alignment
  • Profiling
  • Read mapping
  • Pooling
  • Assembling
  • Binning
  • Annotation
  • Genome operation
  • Genome quality check and annotation
  • Strain-level analysis
  • Pipeline suites
  • Visualisation
• Contributing
  • Overview
  • Tutorial
  • Templates
  • Notes