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Commit 3aac3bfe authored by Florian Centler's avatar Florian Centler

Update README.md

parent 913900f1
# CMP
A custom-made adaptable analysis pipeline for metagenomics data
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A custom-made adaptable analysis pipeline for metagenomics data
## Getting Started
The latest version of CMP can be obtained via git:
```
git clone https://git.ufz.de/UMBSysBio/cmp.git
```
### Prerequisites
CMP makes use of a number of software packages, which need to be available on the local machine, including:
* Prodigal
* FastQC
* FastX Tool Kit
* Trimmomatic
* Velvet
* Metaxa2 (and supporting tools)
* MetaPhlAn
* Bowtie2
* ABySS
* MaxBin2
* CheckM
* bam2fastq
* samtools
* bedtools
* bamtools
* BBMap
* Diamond
* MEGAN
If the usage of other tools is desired, they can easily be replaced.
### Installing
An installation bash script is provided which installs all required tools (except for Diamond and MEGAN) for the standard CMP (see above):
```
install.sh
```
Please check comments in the script for further instructions.
## Author
* **Daniela Becker**, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
Contact: daniela.taraba@ufz.de
## License
This project is licensed under the GNU General Public License v3.0 - see the [LICENSE](LICENSE) file for details
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