Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples
Pipeline for metagenomic identification of dietary DNA from archaeological samples.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. nf-core/archaeodiet performs identification and authentication of putative 'dietary' taxa based on DNA from archaeological metagenomic samples.
iii. Download the pipeline and test it on a minimal dataset with a single command
bashnextflow run nf-core/archaeodiet -profile test,
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
bashnextflow run nf-core/archaeodiet -profile --input '*.fastq.gz'
See usage docs for all of the available options when running the pipeline.
Development of this pipeline was supported by the ERC Starting Grant project (FoodTransforms) ERC-2015-StG 678901 funded by the European Research Council awarded to Philipp W. Stockhammer (Ludwig Maximilian University, Munich).