ArticleF1000Research2017
Investigation of chimeric reads using the MinION.
Article in F1000Research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- ReadChop: a high-performance demultiplexer for long-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Filtering of artificial chimeric reads generated by ligation preparation method of nanopore sequencing.iScience · 2026Article
- Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia.The Journal of molecular diagnostics : JMD · 2026Article
- Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.Microbiology spectrum · 2026Article
- Efficient multi-kilobase knock-ins in mice and cell lines using CRISPR/Cas9 and rAAV donors with unbiased whole-genome characterization by LOCK-seq.Nucleic acids research · 2026Article
- ESPeR-seq: Extremely Sensitive and Pure, End-to-end, RNA-seq library preparation.bioRxiv : the preprint server for biology · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Detecting foldback artifacts in long-reads.BMC genomics · 2026Article
- Long read nanopore DNA sequencing with adaptive sampling to identify tyrosine kinase fusion genes.Leukemia · 2026Article
- Detecting Foldback Artifacts in Long-reads.bioRxiv : the preprint server for biology · 2025Article
- Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.BMC medical genomics · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- Article
- Flexiplex: a versatile demultiplexer and search tool for omics data.Bioinformatics (Oxford, England) · 2024Article
- Comment on "DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction".Analytical chemistry · 2024Article
- Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci.PLoS pathogens · 2023Article
- Article
- Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.GigaScience · 2023Article
- AmpSeqR: an R package for amplicon deep sequencing data analysis.F1000Research · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Following a nanopore sequencing run of PCR products of three amplicons less than 1kb, an abundance of reads failed quality control due to template/complement mismatch. A BLAST search demonstrated that some of the failed reads mapped to two different genes -- an unexpected observation, given that PCR was carried out separately for each amplicon. A further investigation was carried out specifically to search for chimeric reads, using separate barcodes for each amplicon and trying two different ligation methods prior to sample loading. Despite the separation of ligation products, chimeric reads formed from different amplicons were still observed in the base-called sequence. The long-read nature of nanopore sequencing presents an effective tool for the discovery and filtering of chimeric reads. We have found that at least 1.7% of reads prepared using the Nanopore LSK002 2D Ligation Kit include post-amplification chimeric elements. This finding has potential implications for other amplicon sequencing technologies, as the process is unlikely to be specific to the sample preparation used for nanopore sequencing.
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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.