Download
Share
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Hundo: a Snakemake workflow for microbial community sequence data

, , ,
  Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States
DOI
10.7287/peerj.preprints.27272v1
Published
Accepted
Subject Areas
Bioinformatics
Keywords
16S, ITS, 18S, metagenome
Copyright
© 2018 Brown et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Brown J, Zavoshy N, Brislawn CJ, McCue LA. 2018. Hundo: a Snakemake workflow for microbial community sequence data. PeerJ Preprints 6:e27272v1

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.

Author Comment

This is a preprint submission to PeerJ Preprints.

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Joseph Brown conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Nicole Zavoshy conceived and designed the experiments, performed the experiments, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Colin J Brislawn conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Lee Ann McCue conceived and designed the experiments, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Hundo is available at https://github.com/pnnl/hundo (DOI 10.5281/zenodo.1429364).

Data, raw and processed, used in this manuscript are available via Open Science Framework at https://osf.io/T4NC7/ (DOI 10.17605/OSF.IO/T4NC7).

Funding

This research was supported by the Microbiomes in Transition Initiative LDRD Program at the Pacific Northwest National Laboratory, a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC06-76RL01830. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies
Download
Content
Alert
Just enter your email

Download article

Hundo: a Snakemake workflow for microbial community sequence data
PDF Save to Mendeley RIS XML BibTeX
10 Citations   Views   Downloads