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Extending long-range phasing and haplotype library imputation algorithms to large and heterogeneous datasets
BackgroundWe describe the latest improvements to the long-range phasing (LRP) and haplotype library imputation (HLI) algorithms for successful...
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Phasing out live poultry market trading policy in China: characteristics of chicken consumption, decision-making behavior, and consumer cluster analysis
With the emergence of avian influenza viruses, many Chinese cities periodically close the live poultry markets to restrict the trade of live chicken....
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A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients
Previous studies have conducted time course characterization of murine colitis models through transcriptional profiling of differential expression....
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Variant phasing and haplotypic expression from long-read sequencing in maize
Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic...
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Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks
Sample recruitment for research consortia, biobanks, and personal genomics companies span years, necessitating genoty** in batches, using different...
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Exploring effective approaches for haplotype block phasing
BackgroundKnowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for...
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Role of phasiRNAs from two distinct phasing frames of GhMYB2 loci in cis- gene regulation in the cotton genome
BackgroundPhased small interfering RNA (phasiRNA) is primarily derived from the 22-nt miRNA targeting loci. GhMYB2 , a gene with potential roles in...
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Haploty**-Assisted Diploid Assembly and Variant Detection with Linked Reads
Phasing is essential for determining the origins of each set of alleles in the whole-genome sequencing data of individuals. As such, it provides...
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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present...
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Sequencing and Assembly of Polyploid Genomes
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations...
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Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a...
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A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy
BackgroundLow-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and...
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Targeted Locus Amplification and Haploty**
Targeted locus amplification (TLA) allows for the detection of all genetic variation (including structural variation) in a genomic region of...
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Rare variant phasing using paired tumor:normal sequence data
BackgroundIn standard high throughput sequencing analysis, genetic variants are not assigned to a homologous chromosome of origin. This process,...
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Phasing quality assessment in a brown layer population through family- and population-based software
BackgroundHaplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring...
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Haplotype-resolved assembly of a pig genome using single-sperm sequencing
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed...
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Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. Single-cell RNA sequencing (scRNA-seq)...
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nPoRe: n-polymer realigner for improved pileup-based variant calling
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor....
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HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
BackgroundIdentifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and...
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The solution surface of the Li-Stephens haplotype copying model
The Li-Stephens (LS) haplotype copying model forms the basis of a number of important statistical inference procedures in genetics. LS is a...
