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


Document Type



Biochemistry | Bioinformatics | Computational Biology | Ecology and Evolutionary Biology | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides


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.


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 (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

DOI of Published Version



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

Link to Article in PubMed

PubMed ID


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.