ArticleBMC genomics2019
DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
- An X-to-autosome-to-Y chromosome amplified retrogene family functions in spermatids.Current biology : CB · 2026Article
- Detection of sex chromosomes in Tephritid pests using R-CQ and KAMY, two computational methods to support generic pest management applications.Insect science · 2026Article
- Chromosome-Level Sex-Specific Genome Assemblies of Onthophagus binodis Provide Insight into Scarab Sex Chromosomes.Genome biology and evolution · 2026Article
- EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.NAR genomics and bioinformatics · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- An effective strategy for assembling the sex-limited chromosome.GigaScience · 2024Article
- Possible stochastic sex determination in Bursaphelenchus nematodes.Nature communications · 2022Article
- Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.BMC genomics · 2022Article
- Evaluation of four methods to identify the homozygotic sex chromosome in small populations.BMC genomics · 2022Article
- Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.Molecular biology and evolution · 2021Article
- Effective sequence similarity detection with strobemers.Genome research · 2021Article
- Representation ofJournal of computational biology : a journal of computational molecular cell biology · 2021Article
- A novelLife science alliance · 2021Article
- Dynamic evolution of great ape Y chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAlthough the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references.
resultsWe develop a k-mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal. We evaluate the performance of DiscoverY on human and gorilla genomes, across different sequencing platforms including Illumina, 10X, and PacBio. In the cases where the male and female data are of high quality, DiscoverY has a high precision and recall and outperforms existing methods. For cases when a high quality female reference is not available, we quantify the effect of using draft reference or even just raw sequencing reads from a female.
conclusionDiscoverY is an effective method to isolate Y-specific contigs from a whole-genome assembly. However, regions homologous to the X chromosome remain difficult to detect.
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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.