ArticleGenome biology2014
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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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.
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Who cites it
28 citing papers in PubMed.
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Anchorage accurately assembles anchor-flanked synthetic long reads.Algorithms for molecular biology : AMB · 2025Article
- Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2024Article
- Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers.Functional & integrative genomics · 2023Article
- Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.Applied and environmental microbiology · 2021Review
- Review
- MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.Nucleic acids research · 2021Article
- Article
- Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.Communications biology · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution.Nature communications · 2020Article
- An integrated software for virus community sequencing data analysis.BMC genomics · 2020Article
- Children With Cystic Fibrosis Are Infected With Multiple Subpopulations of Mycobacterium abscessus With Different Antimicrobial Resistance Profiles.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2019Article
- Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.Nature reviews. Genetics · 2018Review
- Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias.Nature biotechnology · 2018Article
- HLA genotyping by next-generation sequencing of complementary DNA.BMC genomics · 2017Article
- Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.BMC genomics · 2017Article
- Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
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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.