DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies
Authors: Kateryna D Makova
Marta Tomaszkiewicz
Natasha Stopa
Samarth Rangavittal
Kristoffer Sahlin
Paul Medvedev
Journal: BMC Genomics (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: Genome assembly; Male genome; Y chromosome.
Affiliations: Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA., Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16802, USA., Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. ., The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA. ., Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16802, USA. ., Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA. .

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. 

Retracted: No

PubPeer comments:
 I think the blue rectangle in the legend for Figure 1 should say  Female Illumina rather than  Female hg38 ? , 
 #1 Care to explain your reasoning? The figure labeling seems to fit with the description in the text:  The best accuracy was obtained with the 10X male and hg38 female, with a precision u200999.99% and recall of 82% , 
 #2 #1 I think you have a good point. I thought the color and shape seemed to be labeled in different ways. However, as described in the text, they use the genome reference hg38 (without chrY) for comparison as well ( *The first was the female reference obtained by removing the Y chromosome from the high-quality hg38 reference*. ). In other words, there is intentionally not an Illumina-to-Illumina comparison (although there is a female Illumina dataset listed in Table 1). So, I think this is in fact OK. I apologize for the confusion, but I hope this helps other readers. ,