دورية أكاديمية
DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies
| العنوان: | DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies |
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| المؤلفون: | Samarth Rangavittal, Natasha Stopa, Marta Tomaszkiewicz, Kristoffer Sahlin, Kateryna D. Makova, Paul Medvedev |
| المصدر: | BMC Genomics, Vol 20, Iss 1, Pp 1-11 (2019) |
| بيانات النشر: | BMC, 2019. |
| سنة النشر: | 2019 |
| المجموعة: | LCC:Biotechnology LCC:Genetics |
| مصطلحات موضوعية: | Genome assembly, Y chromosome, Male genome, Biotechnology, TP248.13-248.65, Genetics, QH426-470 |
| الوصف: | Abstract Background Although 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. Results We 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. Conclusion DiscoverY 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2164 |
| Relation: | http://link.springer.com/article/10.1186/s12864-019-5996-3; https://doaj.org/toc/1471-2164 |
| DOI: | 10.1186/s12864-019-5996-3 |
| URL الوصول: | https://doaj.org/article/854294d6ad0240a4be26eba88f63087a |
| رقم الأكسشن: | edsdoj.854294d6ad0240a4be26eba88f63087a |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 14712164 |
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| DOI: | 10.1186/s12864-019-5996-3 |