This is a comprehensive pipeline for amplicon-based metagenomics integrating in a Snakemake workflow the best functions of many tools. It enables performant and reproducibile processing of 16S rRNA or ITS Illumina paired-end reads. The whole process from local .fastq or SRA depository files to generation of basic visualization plots, including quality control plots of intermediate steps, is covered.
git clone https://github.com/metagenlab/zAMP.git
pip install -e zAMP
$ zamp -h
Usage: zamp [OPTIONS] COMMAND [ARGS]...
Snakemake pipeline designed for convenient, reproducible and scalable
amplicon-based metagenomics
For more options, run: zamp command --help
Options:
-v, --version Show the version and exit.
-h, --help Show this message and exit.
Commands:
db Prepare database files for zAMP
run Run zAMP
citation Print zAMP and tools citations
zamp run -i samples.tsv -db greengenes2 --fw-primer CCTACGGGNGGCWGCAG --rv-primer GACTACHVGGGTATCTAATCC