YAMP: a containerized workflow enabling reproducibility in metagenomics research
“Yet Another Metagenomics Pipeline” (YAMP), a ready-to-use containerized workflow that, using state-of-the-art tools, processes raw shotgun metagenomics sequencing data up to the taxonomic and functional annotation. YAMP is implemented in Nextflow and is accompanied by a Docker and a Singularity container. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.
YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. The YAMP script, parameters, and documentation are available at https://github.com/alesssia/YAMP.
If you use YAMP for research purpose, please cite:
Visconti, Alessia, et al. “YAMP: a containerized workflow enabling reproducibility in metagenomics research” GigaScience 7(7) (2018), DOI:10.1093/gigascience/giy072