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Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq
The successful accomplishment of the first telomere-to-telomere human genome assembly, T2T-CHM13, marked a milestone in achieving completeness of the...
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GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C
Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers...
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Accurate genome-wide phasing from IBD data
As genotype databases increase in size, so too do the number of detectable segments of identity by descent (IBD): segments of the genome where two...
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Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing
BackgroundWhole genome sequencing using the long-read Oxford Nanopore Technologies (ONT) MinION sequencer provides a cost-effective option for...
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Read-Based Phasing and Analysis of Phased Variants with WhatsHap
WhatsHap is a command-line tool for phasing and phasing-related tasks. It allows to infer haplotypes in diploid and polyploid samples based on...
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HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data
Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however...
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Phasing DNA Methylation
Haploty** enables the study of allele-specific events. Heterozygous variants, primarily single nucleotide variants (SNVs), enable the assignment of...
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DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing
Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA...
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Benchmarking phasing software with a whole-genome sequenced cattle pedigree
BackgroundAccurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are...
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Full-Length Transcript Phasing with Third-Generation Sequencing
Haploty** individual full-length transcripts can be important in diagnosis and treatment of certain genetic diseases. One set of diseases, repeat...
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Ab initio phasing macromolecular structures using electron-counted MicroED data
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct...
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Low-Cost Genome-Scale Phasing with Barcode-Linked Sequencing
Complete comprehension of clinically relevant variation among human genomes is likely only to come from sequencing platforms that are cost-efficient,...
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trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios
BackgroundWhen analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be beneficial when trying to...
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Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach
This chapter describes the usage of homologizer to phase gene copies into polyploid subgenomes. Allopolyploids contain multiple copies of each...
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Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data
BackgroundMost animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In...
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Failing the four-gamete test enables exact phasing: the Corners’ Algorithm
BackgroundFailing the four-gamete test for two polymorphic DNA markers is an indication that two or three rather than four haplotypes segregate in...
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nPhase: an accurate and contiguous phasing method for polyploids
While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing...
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Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing...
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GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
GRIDSS2 is the first structural variant caller to explicitly report single breakends—breakpoints in which only one side can be unambiguously...
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Haplotype threading: accurate polyploid phasing from long reads
Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding...
