ArticleNucleic acids research2019
Long-read amplicon denoising.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- The GFI1 Gene Family: Evolution, Structure, and Its Role in Immune Responses.Journal of molecular evolution · 2026Article
- Changes in intra-host mycovirus population diversity after vertical and horizontal transmission.Virus evolution · 2025Article
- Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1AIDS research and human retroviruses · 2024Article
- Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.Nature communications · 2024Article
- Exploiting long read sequencing to detect azole fungicide resistance mutations in Pyrenophora teres using unique molecular identifiers.Scientific reports · 2024Article
- FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus.Journal of molecular evolution · 2024Article
- Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.Clinical & translational immunology · 2024Article
- Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies.Virus evolution · 2024Article
- Combined Multiplexed Phage Display, High-Throughput Sequencing, and Functional Assays as a Platform for Identifying Modulatory VHHs Targeting the FSHR.International journal of molecular sciences · 2023Article
- Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues.Journal of virology · 2023Article
- Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages.Nature communications · 2023Article
- Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators.Plant reproduction · 2023Review
- High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS.ISME communications · 2022Article
- MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis.Bioinformatics (Oxford, England) · 2022Article
- Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies.Science advances · 2022Article
- Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections.Virus evolution · 2021Article
- Article
- A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir.Cell reports. Medicine · 2021Article
- Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells.Nature communications · 2020Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
Long-read next-generation amplicon sequencing shows promise for studying complete genes or genomes from complex and diverse populations. Current long-read sequencing technologies have challenging error profiles, hindering data processing and incorporation into downstream analyses. Here we consider the problem of how to reconstruct, free of sequencing error, the true sequence variants and their associated frequencies from PacBio reads. Called 'amplicon denoising', this problem has been extensively studied for short-read sequencing technologies, but current solutions do not always successfully generalize to long reads with high indel error rates. We introduce two methods: one that runs nearly instantly and is very accurate for medium length reads and high template coverage, and another, slower method that is more robust when reads are very long or coverage is lower. On two Mock Virus Community datasets with ground truth, each sequenced on a different PacBio instrument, and on a number of simulated datasets, we compare our two approaches to each other and to existing algorithms. We outperform all tested methods in accuracy, with competitive run times even for our slower method, successfully discriminating templates that differ by a just single nucleotide. Julia implementations of Fast Amplicon Denoising (FAD) and Robust Amplicon Denoising (RAD), and a webserver interface, are freely available.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.