Hundo: a Snakemake workflow for microbial community sequence data

Abstract

Hundo is a software package that performs quality control and annotation of ribosomal RNA and internal transcribed spacer sequence reads. It provides a comprehensive suite of tools and options that aim to reduce the effort of performing robust sequence annotation while obtaining the maximum amount of data provenance to ensure replicability. The software package performing annotation is implemented in Python, the analytical workflow is implemented in Snakemake, and dependencies are installed via Bioconda. Extensive documentation and the full source code are available under the MIT license at: https://github.com/pnnl/hundo.