UMMS Affiliation
Program in Bioinformatics and Integrative Biology; Division of Transfusion Medicine, Department of Medicine; Graduate School of Biomedical Sciences, Bioinformatics and Computational Biology Program; Graduate School of Biomedical Sciences, MD/PhD Program
Publication Date
2-28-2018
Document Type
Article
Disciplines
Biochemistry | Bioinformatics | Computational Biology | Ecology and Evolutionary Biology | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides
Abstract
PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences differing by a single nucleotide polymorphism. In bacterial populations, single-base resolution can provide improved resolution towards species and strains. Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single base. It outperforms current software, particularly at low frequencies and at low input read depths, whether resolving single-base differences or traditional OTUs. SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic information.
Keywords
Massively Parallel (Deep) Sequencing
Rights and Permissions
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI of Published Version
10.1093/nar/gkx1201
Source
Nucleic Acids Res. 2018 Feb 28;46(4):e21. doi: 10.1093/nar/gkx1201. Link to article on publisher's site
Journal/Book/Conference Title
Nucleic acids research
Related Resources
PubMed ID
29202193
Repository Citation
Hathaway, Nicholas J.; Parobek, Christian M.; Juliano, Jonathan J.; and Bailey, Jeffrey A., "SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing" (2018). Open Access Articles. 3389.
https://escholarship.umassmed.edu/oapubs/3389
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Biochemistry Commons, Bioinformatics Commons, Computational Biology Commons, Ecology and Evolutionary Biology Commons, Molecular Biology Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons