ArticleBioinformatics (Oxford, England)2022
ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 49 citations in OpenAlex.
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- A framework for optimising arthropod DNA quality and quantity for modern sequencing tools using hard ticks (Ixodidae).Parasitology research · 2026Article
- HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly.iMetaOmics · 2025Article
- Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.Nature communications · 2025Article
- SKiM: accurately classifying metagenomic ONT reads in limited memory.Bioinformatics (Oxford, England) · 2025Article
- A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.Molecular ecology resources · 2025Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.).BMC genomics · 2025Article
- Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals.Computational and structural biotechnology journal · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Real-time and programmable transcriptome sequencing with PROFIT-seq.Nature cell biology · 2024Article
- Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection.The Journal of molecular diagnostics : JMD · 2024Review
- RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization.Bioinformatics (Oxford, England) · 2024Article
- A case of an Angelman-syndrome caused by an intragenic duplication of UBE3A uncovered by adaptive nanopore sequencing.Clinical epigenetics · 2024Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 2024Article
- Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER.Nature communications · 2024Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.
resultsHere, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background. AVAILABILITY AND IMPLEMENTATION: The C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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 OpenQuestion graph.