DNA from peripheral blood samples of these animals was genotyped with the bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data using the 1000 Bull genomes reference population. A genome-wide association study (GWAS) was performed using the...
Whole genome sequencing (WGS) is the comprehensive read and analysis of an entire genome, including non-coding regions of the genome.
Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as ...
Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.
The whole-genome resequencing data yielded 17,295,344 SNPs across the 11 wildM. m. domesticussamples (Additional file1: Table S4). Totally, 143,421 SNPs were distributed in exons, 3,997,285 in introns, and 9,949,066 in intergenic regions. The genome resequencing analysis from 9 wildM. ...
SMC++ is a program for estimating the size history of populations from whole genome sequence data. Quick start guide Follow theinstallation instructions. Convert your VCF(s) to the SMC++ input format withvcf2smc: $ smc++ vcf2smc my.data.vcf.gz out/chr1.smc.gz chr1 Pop1:S1,S2 ...
Whole genome sequencing (WGS) has increased in popularity and decreased in cost over the past decade, rendering this approach as a viable and sensitive method for variant detection. In addition to its utility for single nucleotide variant detection, WGS data has the potential to detect Copy Number...
diCal2is a software program for inferring parameters of demographic histories from whole genome sequence data. To this end, it combines several demography-aware conditional sampling distributions in a composite likelihood framework. This composite likelihood is then used in an EM algorithm, to find the...
et al. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics 19, 613 (2018). PubMed PubMed Central Google Scholar Gan, M., Liu, Q., Yang, C., Gao, Q. & Luo, T. Deep whole-genome sequencing to detect mixed infection of Mycobacterium ...
Stage I whole-genome sequence data processing Sequence reads were processed and aligned to the reference genome (hg19) with the BWA algorithm and processed with Picard (http://picard.sourceforge.net). Polymorphic SNP and indel sites and genotypes were called with the HaplotypeCaller from GATK v3.1...