Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

(2020) Edward S Rice et al.   GigaScience

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity

(2019) Wai Yee Low et al.   Nature Communications

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

(2018) Dong-Dong Wu et al.   Nature Ecology & Evolution

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

(2017) Ivica Medugorac et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Single nucleotide polymorphisms in the bovine MHC region of Japanese Black cattle are associated with bovine leukemia virus proviral load

(2017) Shin-nosuke Takeshima et al.   Retrovirology

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A clone-free, single molecule map of the domestic cow (Bos taurus) genome

(2015) Shiguo Zhou et al.   BMC GENOMICS

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

(2015) Li Ma et al.   PLoS Genetics

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Prevalence of the prion protein gene E211K variant in U.S. cattle

(2008) Michael P Heaton et al.   BMC Veterinary Research