https://github.com/husonlab/megmap
Metagenome mapping utilities
https://github.com/husonlab/megmap
Last synced: 19 days ago
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Metagenome mapping utilities
- Host: GitHub
- URL: https://github.com/husonlab/megmap
- Owner: husonlab
- License: gpl-3.0
- Created: 2022-09-19T10:04:03.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-11-03T20:51:29.000Z (over 3 years ago)
- Last Synced: 2023-05-11T16:25:15.174Z (about 3 years ago)
- Language: Python
- Size: 80.1 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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.
[](https://www.python.org/)
## 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](#features)
* [Workflows](#workflows)
* [Main workflow](#main-workflow)
* [Workflow by input file type](#workflow-by-input-file-type)
* [Workflow by bypass mode](#workflow-by-bypass-mode)
* [Workflow of the resume option](#workflow-of-the-resume-option)
* [Requirements](#requirements)
* [Software](#software)
* [Other](#other)
* [Automated Installation](#Automated-installation)
## Requirements ##
### Software ###
1. [DIAMOND](https://github.com/weizhongli/cdhit)
Please install the required software in a location in your `$PATH`
## Installation
----
## via Conda ##
```sh
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
```
----
## Automated Installation ##
```sh
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
```
----
## License
GPL-3.0
**Free Software!**
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