MiGA Manual
AboutCodebaseMiGA Online
Primary version
Primary version
  • Introduction
  • Part I: What is MiGA?
    • How can MiGA help me?
    • Who is using MiGA?
    • Who is behind MiGA?
    • Definitions
  • Part II: Getting started
    • Requirements
      • Using Homebrew
      • Using apt-get
      • Using Conda
      • Installing from source
      • MyTaxa Utils
    • Installation
    • MiGA types
    • Input data
    • Distances
    • Clustering
  • Part III: Interfaces
    • MiGA API
    • MiGA CLI
    • MiGA Web
  • Part IV: Deploying examples
    • RefSeq in MiGA
    • Build a clade collection
    • Launching daemons
    • Setting up MiGA in a cluster
  • Part V: Additional details
    • Advanced configuration
    • MiGA workflow
    • Metadata
    • External Software
  • Part VI: Workflows
    • Quality
    • Dereplicate
    • Classify
    • Preprocess
    • Index
    • Summaries
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  1. Part VI: Workflows

Preprocess

PreviousClassifyNextIndex

Last updated 4 years ago

This workflow automates the preprocessing of your genomic or metagenomic datasets.

To execute the workflow, run:

miga preproc_wf -o my_project -i raw_reads_single path/to/reads/*.fastq

Supported inputs include:

  • raw_reads_single: Single raw reads in a single FastQ file

  • raw_reads_paired: Paired raw reads in two FastQ files

  • trimmed_reads_single: Single trimmed reads in a single FastA file

  • trimmed_reads_paired: Paired trimmed reads in two FastA files

  • trimmed_reads_interleaved: Paired trimmed reads in a single FastA file

  • assembly: Assembled contigs or scaffolds in FastA format

For additional options, run:

miga preproc_wf -h

Expected output

Once your run is complete, you may expect the for cds, assembly, essential_genes, and ssu. Additionally all the intermediate files are preserved, including assemblies, predicted genes, and detected essential and ribosomal genes.

standard summaries