ArticleNucleic acids research2018
SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed.
- Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees.Journal of virology · 2019Trial
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- Toward an Open Analysis Ecosystem for Plasmodium Genomic Epidemiology.The American journal of tropical medicine and hygiene · 2026Article
- CXCR6+ CD127- Tr1 cells balance immunity and persistence in Plasmodium falciparum infection.The Journal of clinical investigation · 2026Article
- Continental-scale genomic surveillance of Plasmodium falciparum malaria across sub-Saharan Africa with rapid nanopore sequencing.Nature communications · 2026Article
- Spatiotemporal antimalarial drug resistance saturation and emerging artemisinin tolerance in western Kenya during a pilot multiple first-line treatment study.Scientific reports · 2026Article
- Complexity of Infection andmedRxiv : the preprint server for health sciences · 2026Article
- Haplotype diversity ofFrontiers in parasitology · 2026Article
- The Portable Microhaplotype Object and Tools.bioRxiv : the preprint server for biology · 2025Article
- Toward Setting Minimum and Optimal Data to Report for Malaria Molecular Surveillance with Targeted Sequencing: The "What" and "Why".The American journal of tropical medicine and hygiene · 2025Article
- SARS-CoV-2 mutant spectrum complexity is an epidemiologically evolvable trait.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- CXCR6bioRxiv : the preprint server for biology · 2025Article
- High voltage-gated sodium channel gene diversity in Aedes albopictus across Brazil.Scientific reports · 2025Article
- Plasmodium falciparum genetic diversity and multiplicity of infection in northern and southern Ghana assessed by amplicon sequencing.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and population genomics.BMC research notes · 2025Article
- Article
- Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health.Scientific reports · 2025Article
- Sensitive and modular amplicon sequencing ofbioRxiv : the preprint server for biology · 2025Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
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.
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