megmap

Attention: This program is under heavy development, in particular:

• There will be many bugs (please let us know about any that you find).
• There are several missing features that are still to be added (please let us know about things that you would like).
• File formats will change. Before opening a new issue here, please check the appropriate already exits issues and commenting on a thread there.

megmap User Manual

megmap help you perform metegenomic analysis against special purpose database

If you use megmap in your work, please cite the megmap paper:

Contents

• Features
• Workflows
  • Main workflow
  • Workflow by input file type
  • Workflow by bypass mode
  • Workflow of the resume option
• Requirements
  • Software
  • Other
• Automated Installation

Requirements

Software

1. DIAMOND Please install the required software in a location in your $PATH

Installation

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via Conda

1. Create environment and install.
      conda create --name megmap -c anupam__gautam megmap -c conda-forge -c anaconda -c etetoolkit -c bioconda -c defaults megmap

2. Activate environment and use.
      conda activate megmap

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Automated Installation

1. Clone megmap git.
      git clone https://github.com/husonlab/megmap.git

2. Move to the megmap directory.
      cd megmap`

3. Create conda environment with require dependency. 
      conda env create -n megmap --file megmap_2022.09_py10_conda.yaml
      conda activate megmap

Complete Usage

megmap -h
Usage: megmap [options] infile

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License

GPL-3.0

Free Software!