This is basic pipeline to de-novo assemble metagenomic sequencing data. It is written in Snakemake and it was adapted to include ancient DNA specific steps, such as the evaluation of the presence of ancient DNA damage using PyDamage that are usually absent in metagenome assembly pipelines. This pipeline heavily borrows ideas from the Nextflow pipeline MADMAN, which was deprecated and its ideas further developed in the Nextflow pipeline nf-core/mag.
To be able to run the pipeline, Snakemake with a minimal version of 7.0 is necessary. The easiest way to install the dependencies of this program and to have reproducible results is to create a new conda environment using the environment file provided with it.
wget https://raw.githubusercontent.com/alexhbnr/ancient_metagenome_assembly/main/environment.yml
conda env create -f environment.yml
After activating the environment using
conda activate ancient_metagenome_assembly
the necessary Python environment has been created.
Next, the pipeline itself needs to be downloaded. This can be easily down by cloning this repository to your computer via git
git clone https://github.com/alexhbnr/ancient_metagenome_assembly.git
or by downloading the zip file and extracting this
wget -O ancient_metagenome_assembly.zip https://github.com/alexhbnr/ancient_metagenome_assembly/archive/refs/heads/main.zip
unzip ancient_metagenome_assembly.zip
Finally, the configuration file and sample table have to be provided. Templates for these can be
found in config/config.yaml for the configuration file and in test/samples.tsv for the sample
table.
To run a test case using the sequencing data of the Chimpanzee dental calculus sample CDC010 published by James Fellow Yates et al. (PNAS, 2021; doi:10.1073/pnas.2021655118), we will need to download the FastQ files from ENA:
wget -O test/ERR3579712_1.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR357/002/ERR3579712/ERR3579712_1.fastq.gz
wget -O test/ERR3579712_2.fastq.gz http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR357/002/ERR3579712/ERR3579712_2.fastq.gz
To start the pipeline, we run
snakemake --use-conda --conda-prefix conda -j 8
This will automatically evaluate the entries in the configuration file config/config.yaml and use
the sample CDC10 as input. The temporary files are written into the folder tmp and the results
in the folder results.
By activating the options --use-conda, snakemake will download and install the programs
necessary to run the pipeline via conda and store them into the folder conda. This step will only
happen once, at the first time or when you change the folder for storing these conda environments
using --conda-prefix.