Haplotype assembly
-
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes.
26p viarchimedes 26-01-2022 10 0 Download
-
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.
27p viarchimedes 26-01-2022 14 0 Download
-
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets.
20p viarchimedes 26-01-2022 10 0 Download
-
Assembly of haplotypes polyploid organisms is considerably more difficult than in the case of diploids. Hence, scalable and accurate schemes with provable performance are desired for haplotype assembly of both diploid and polyploid organisms.
15p vibeauty 23-10-2021 9 0 Download
-
Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny.
13p vikentucky2711 24-11-2020 9 1 Download
-
Single individual haplotype problem refers to reconstructing haplotypes of an individual based on several input fragments sequenced from a specified chromosome.
15p vikentucky2711 24-11-2020 8 1 Download
-
Genetic variations predispose individuals to hereditary diseases, play important role in the development of complex diseases, and impact drug metabolism. The full information about the DNA variations in the genome of an individual is given by haplotypes, the ordered lists of single nucleotide polymorphisms (SNPs) located on chromosomes.
10p vikentucky2711 24-11-2020 10 1 Download
-
Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly.
10p vicoachella2711 27-10-2020 7 1 Download
-
Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays cheaper to produce and more widely available than ever before, have been used to reduce the fragmentation of the assembled haplotypes since their ability to span several variants along the genome.
19p viconnecticut2711 28-10-2020 17 1 Download
-
Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes.
11p viconnecticut2711 28-10-2020 9 1 Download
-
Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity.
13p vicolorado2711 23-10-2020 8 1 Download
-
Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads.
18p vicolorado2711 22-10-2020 5 0 Download
-
In this paper, Harmony Search (HS) is considered a clustering approach. Extensive computational experiments indicate that the designed HS algorithm achieves a higher accuracy than the genetic algorithm (GA) or particle swarm optimization (PSO) to the MEC model in most cases.
9p girlsseek 27-02-2019 26 0 Download