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HapFlow: Visualising haplotypes in sequencing data

, , ,
  Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
DOI
10.7287/peerj.preprints.895v1
Published
Accepted
Subject Areas
Bioinformatics, Genomics, Microbiology
Keywords
Haplotype, Genome sequencing, Mixed infections
Copyright
© 2015 Sullivan 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
Sullivan MJ, Bachmann NL, Timms P, Polkinghorne A. 2015. HapFlow: Visualising haplotypes in sequencing data. PeerJ PrePrints 3:e895v1

Abstract

Summary: HapFlow is a python application for visualising haplotypes present in high-throughput sequencing data. HapFlow identifies nucleotide variant profiles in raw read sequences and creates an abstract visual representation of these profiles to make haplotypes easier to identify. Availablity: HapFlow is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from github (http://mjsull.github.io/HapFlow).

Author Comment

This article describes a software program for visualizing DNA variations in sequence data. We are making the software available as a pre-print article in order to get feedback from the community to optimize and improve the program. The article will be submitted to a journal for review. Contact: apolking@usc.edu.au

Additional Information

Competing Interests

The authors declare they have no competing interests.

Author Contributions

Mitchell J Sullivan performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Nathan L Bachmann performed the experiments, analyzed the data, reviewed drafts of the paper.

Peter Timms conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Adam Polkinghorne conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding the deposition of related data:

GitHub (http://mjsull.github.io/HapFlow)

Funding

This work was supported by an Australian Research Council Discovery Grant (DP130102066) and a Queensland Department of Environment and Heritage Protection Koala Research Grant (KRG18) awarded to AP and PT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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HapFlow: Visualising haplotypes in sequencing data
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