ArticleMethods in molecular biology (Clifton, N.J.)2023
Chromosome-Length Haplotypes with StrandPhaseR and Strand-seq.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.Nucleic acids research · 2026Article
- Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.Nucleic acids research · 2025Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Phased nanopore assembly with Shasta and modular graph phasing with GFAse.Genome research · 2024Article
- Phased nanopore assembly with Shasta and modular graph phasing with GFAse.bioRxiv : the preprint server for biology · 2023Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Dense local haplotypes can now readily be extracted from long-read or droplet-based sequence data. However, these methods struggle to combine subchromosomal haplotype blocks into global chromosome-length haplotypes. Strand-seq is a single cell sequencing technique that uses read orientation to capture sparse global phase information by sequencing only one of two DNA strands for each parental homolog. In combination with dense local haplotypes from other technologies, Strand-seq data can be used to obtain complete chromosome-length phase information. In this chapter, we run the R package StrandPhaseR to phase SNVs using publicly available sequence data for sample HG005 of the Genome in a Bottle project.
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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.