Haplotype-Phased Common Marmoset Embryonic Stem Cells for Genome Editing Using CRISPR/Cas9Callithrix jacchustransgenicsembryonic stem cellshaplotype phasingCRISPR/Cas9model organismsmarmosetinduced neurons (iNs)Due to anatomical and physiological similarities to humans, the common marmoset (Callithrix jacchus) ...
one primary assembly representing a mosaic of homolo-gous haplotypes, and one alternate assembly composed of short haplotype-specific contigs (haplotigs) for alleles absent from the pri-mary assembly. The alternate assembly is often
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce
inPHAP phased haplotype view for the 100-kb region on chromosome 2 spanning the genes ALMS1 , NAT8 and ALMS1P , after filtering of rare variants with a frequency < 0 .5% across the 1096 human individuals of Phase 1 of the 1000 Genomes Project [24]. The bases A,C,T,G are colored...
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies. It was originally developed for constructing thesyndipbenchmark dataset and has been applied to other phased assemblies, too. Dipcall can call small variants and long INDELs as long as they are conta...
James A StapletonJeongwoon KimJohn P HamiltonMing WuLuiz C IrberRohan MaddamsettiBryan BrineyLinsey NewtonDennis R BurtonC Titus BrownCold Spring Harbor LaboratoryStapleton, J.A. et al. Haplotype-phased synthetic long reads from short-read sequenc- ing. bioRxiv, doi: http://dx.doi.org/...
We report herethe first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid ...
A chromosome-level, haplotype-phased genome assembly for Vanilla planifolia highlights that partial endoreplication challenges accurate whole genome assemblydoi:10.1016/j.xplc.2022.100330Q. PietG. DrocW. MarandeG. SarahS. BocsC. KloppM. Bourge...
Haplotype Blocks of Phased DataPhasedGenotypeMatrix
Haplotype network of four human polymorphic inversions from phased HapMap SNP data showing unique or recurrent origins.Cristina, AguadoMagdalena, GayàVidalSergi, VillatoroMeritxell, OlivaDavid, IzquierdoCarla, GinerDelgadoVíctor, MontalvoJudit, GarcíaGonzález...