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First near complete haplotype phased genome assembly of River buffalo ( Bubalus bubalis )

https://doi.org/10.1101/618785
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nbt.4277openalex-snapshot
De novo assembly of haplotype-resolved genomes with trio binning
inferredcites →https://doi.org/10.1038/ng.3802openalex-snapshot
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/nrg3373openalex-snapshot
Phenotypic impact of genomic structural variation: insights from and for human disease
inferredcites →https://doi.org/10.1038/nrg3933openalex-snapshot
Genetic variation and the de novo assembly of human genomes
inferredcites →https://doi.org/10.1038/s41467-018-08260-0openalex-snapshot
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
inferredcites →https://doi.org/10.1038/srep39719openalex-snapshot
Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis
inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot
circlize implements and enhances circular visualization in R
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btw369openalex-snapshot
Assemblytics: a web analytics tool for the detection of variants from an assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btx445openalex-snapshot
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/gigascience/gix085openalex-snapshot
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
inferredcites →https://doi.org/10.1093/gigascience/gix094openalex-snapshot
Draft genome of the gayal, Bos frontalis
inferredcites →https://doi.org/10.1101/306399openalex-snapshot
High coverage genome sequencing and identification of genomic variants in Bengal tiger ( Panthera tigris tigris )
inferredcites →https://doi.org/10.1101/gr.101360.109openalex-snapshot
Assembly of large genomes using second-generation sequencing
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing
inferredcites →https://doi.org/10.1186/s12711-017-0286-5openalex-snapshot
Detection and validation of structural variations in bovine whole-genome sequence data
inferredcites →https://doi.org/10.1186/s12864-015-2007-1openalex-snapshot
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation
inferredcites →https://doi.org/10.1186/s13059-019-1829-6openalex-snapshot
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1004049openalex-snapshot
A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock
inferredcites →https://doi.org/10.2527/af.2016-0002openalex-snapshot
Genomic selection: A paradigm shift in animal breeding
inferredcites →https://doi.org/10.2527/af.2016-0038openalex-snapshot
Metabolic modifiers as performance-enhancing technologies for livestock production
inferredcites →https://doi.org/10.3389/fgene.2014.00037openalex-snapshot
The challenges and importance of structural variation detection in livestock

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-981-16-7531-7_2openalex-snapshot
Water Buffalo Genomic Diversity
inferred← citeshttps://doi.org/10.1007/978-981-16-7531-7_3openalex-snapshot
Advances in Buffalo Breeding: A Journey from Classical Breeding to Genomic Selection
inferred← citeshttps://doi.org/10.1007/s12686-025-01405-6openalex-snapshot
Genome wide mapping of nuclear mitochondrial DNA sequences (NUMTs) and their functionality in domestic water buffalo (Bubalus bubalis)
inferred← citeshttps://doi.org/10.1007/s43538-026-00740-yopenalex-snapshot
Genomic diversity patterns based on effective population size, haplotype blocks and runs of homozygosity in Indian water buffalo breeds
inferred← citeshttps://doi.org/10.1016/j.csbj.2020.07.018openalex-snapshot
Advances in optical mapping for genomic research
inferred← citeshttps://doi.org/10.1080/10495398.2022.2056046openalex-snapshot
Progress and future perspectives of livestock genomics in India: a mini review
inferred← citeshttps://doi.org/10.1093/gigascience/giae053openalex-snapshot
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
inferred← citeshttps://doi.org/10.1093/gigascience/giaf099openalex-snapshot
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection
inferred← citeshttps://doi.org/10.1098/rstb.2020.0168openalex-snapshot
Potential of genomic technologies to improve disease resistance in molluscan aquaculture
inferred← citeshttps://doi.org/10.1101/2024.10.30.620815openalex-snapshot
Quantifying structural variants in chromosomes using landmark-based disparity
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008926openalex-snapshot
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism
inferred← citeshttps://doi.org/10.3389/fpls.2022.947164openalex-snapshot
Reference quality genome sequence of Indian pomegranate cv. ‘Bhagawa’ (Punica granatum L.)
inferred← citeshttps://doi.org/10.3390/genes13050828openalex-snapshot
Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods
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