ReviewGenes2020
Probably Correct: Rescuing Repeats with Short and Long Reads.
Review in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.NAR genomics and bioinformatics · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Improved genotype inference reveals cis- and trans-driven variation in the loss-of-heterozygosity rates in yeast.Genetics · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- A novel H2A-A127 variant is associated with human cancer and enhances tumor-related phenotypes inFrontiers in oncology · 2026Article
- Whole genome sequence analysis ofiScience · 2025Article
- Bamdam: a post-mapping authentication toolkit for ancient metagenomics.Genome biology · 2025Article
- Gapless near Telomer-to-Telomer Assembly ofJournal of fungi (Basel, Switzerland) · 2025Article
- OligoY pipeline for full Y chromosome painting.Briefings in bioinformatics · 2025Article
- Maptcha: an efficient parallel workflow for hybrid genome scaffolding.BMC bioinformatics · 2024Article
- De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus.GigaScience · 2024Article
- Satellite DNAs and human sex chromosome variation.Seminars in cell & developmental biology · 2022Review
- Fragile sites, chromosomal lesions, tandem repeats, and disease.Frontiers in genetics · 2022Review
- Variation and Evolution of Human Centromeres: A Field Guide and Perspective.Annual review of genetics · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ever since the introduction of high-throughput sequencing following the human genome project, assembling short reads into a reference of sufficient quality posed a significant problem as a large portion of the human genome-estimated 50-69%-is repetitive. As a result, a sizable proportion of sequencing reads is multi-mapping, i.e., without a unique placement in the genome. The two key parameters for whether or not a read is multi-mapping are the read length and genome complexity. Long reads are now able to span difficult, heterochromatic regions, including full centromeres, and characterize chromosomes from "telomere to telomere". Moreover, identical reads or repeat arrays can be differentiated based on their epigenetic marks, such as methylation patterns, aiding in the assembly process. This is despite the fact that long reads still contain a modest percentage of sequencing errors, disorienting the aligners and assemblers both in accuracy and speed. Here, I review the proposed and implemented solutions to the repeat resolution and the multi-mapping read problem, as well as the downstream consequences of reference choice, repeat masking, and proper representation of sex chromosomes. I also consider the forthcoming challenges and solutions with regards to long reads, where we expect the shift from the problem of repeat localization within a single individual to the problem of repeat positioning within pangenomes.
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What OpenQuestion 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 OpenQuestion graph.