Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data

Bioinformatics
Fei GuoLusheng Wang

Abstract

Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. The new technologies can provide Single Molecular Sequencing (SMS) data that cover about 90% of positions over chromosomes. However, the SMS data has a higher error rate comparing to 1% error rate for short reads. Thus, it becomes very difficult for SNP calling and haplotype assembly using SMS reads. Most existing technologies do not work properly for the SMS data. In this paper, we develop a progressive approach for SNP calling and haplotype assembly that works very well for the SMS data. Our method can handle more than 200 million non-N bases on Chromosome 1 with millions of reads, more than 100 blocks, each of which contains more than 2 million bases and more than 3K SNP sites on average. Experiment results show that the false discovery rate and false negative rate for our method are 15.7 and 11.0% on NA12878, and 16.5 and 11.0% on NA24385. Moreover, the overall switch errors for our method are 7.26 and 5.21 with average 3378 and 5736 SNP sites per block on NA12878 and NA24385, respectively. Here, we demonstrate that SMS reads alone can generate a high quality solution for both SNP calling and...Continue Reading

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Citations

Sep 26, 2019·Current Gene Therapy·He ZhuangShu-Lin Liu
Jun 18, 2019·Briefings in Functional Genomics·Linlin YuanQuan Zou
Jun 5, 2019·Genome Biology·Jana EblerBenedict Paten
Dec 10, 2020·Computational and Mathematical Methods in Medicine·Yanjuan LiXiaoyan Liu
Apr 7, 2021·Briefings in Bioinformatics·Zilong ZhangQuan Zou
May 26, 2021·Nature Communications·Zhixing FengEric E Schadt

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