Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Authors
Keywords
-
Journal
BMC GENOMICS
Volume 22, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2021-05-19
DOI
10.1186/s12864-021-07554-w
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data
- (2020) Meenu Bhati et al. BMC GENOMICS
- Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
- (2020) Wai Yee Low et al. Nature Communications
- Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
- (2020) Edward S Rice et al. GigaScience
- De novo assembly of the cattle reference genome with single-molecule sequencing
- (2020) Benjamin D Rosen et al. GigaScience
- Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets
- (2020) Justin Bohling Ecology and Evolution
- Regional sequence expansion or collapse in heterozygous genome assemblies
- (2020) Kathryn C. Asalone et al. PLoS Computational Biology
- Errors in long-read assemblies can critically affect protein prediction
- (2019) Mick Watson et al. NATURE BIOTECHNOLOGY
- Similarities and differences between variants called with human reference genome HG19 or HG38
- (2019) Bohu Pan et al. BMC BIOINFORMATICS
- The presence and impact of reference bias on population genomic studies of prehistoric human populations
- (2019) Torsten Günther et al. PLoS Genetics
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- The Third Revolution in Sequencing Technology
- (2018) Erwin L. van Dijk et al. TRENDS IN GENETICS
- A One-Penny Imputed Genome from Next-Generation Reference Panels
- (2018) Brian L. Browning et al. AMERICAN JOURNAL OF HUMAN GENETICS
- De novo assembly of haplotype-resolved genomes with trio binning
- (2018) Sergey Koren et al. NATURE BIOTECHNOLOGY
- Assembly of a pan-genome from deep sequencing of 910 humans of African descent
- (2018) Rachel M. Sherman et al. NATURE GENETICS
- Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB
- (2018) Zhi-Liang Hu et al. NUCLEIC ACIDS RESEARCH
- Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled
- (2018) L. Koufariotis et al. Scientific Reports
- Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
- (2017) Yan Guo et al. GENOMICS
- Genotype Imputation with Millions of Reference Samples
- (2016) Brian L. Browning et al. AMERICAN JOURNAL OF HUMAN GENETICS
- SweepFinder2: increased sensitivity, robustness and flexibility
- (2016) Michael DeGiorgio et al. BIOINFORMATICS
- Detecting recent selective sweeps while controlling for mutation rate and background selection
- (2015) Christian D. Huber et al. MOLECULAR ECOLOGY
- Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
- (2015) Leif Andersson et al. GENOME BIOLOGY
- Second-generation PLINK: rising to the challenge of larger and richer datasets
- (2015) Christopher C Chang et al. GigaScience
- SAMBLASTER: fast duplicate marking and structural variant read extraction
- (2014) G. G. Faust et al. BIOINFORMATICS
- Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle
- (2014) Lingyang Xu et al. MOLECULAR BIOLOGY AND EVOLUTION
- A first look at the Oxford Nanopore MinION sequencer
- (2014) Alexander S. Mikheyev et al. Molecular Ecology Resources
- Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
- (2014) Hans D Daetwyler et al. NATURE GENETICS
- Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle
- (2014) Jared E. Decker et al. PLoS Genetics
- CrossMap: a versatile tool for coordinate conversion between genome assemblies
- (2013) Hao Zhao et al. BIOINFORMATICS
- Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage
- (2013) Sandra Jansen et al. BMC GENOMICS
- A genome-wide scan for signatures of differential artificial selection in ten cattle breeds
- (2013) Sophie Rothammer et al. BMC GENOMICS
- Snakemake--a scalable bioinformatics workflow engine
- (2012) J. Koster et al. BIOINFORMATICS
- Copy number variation of individual cattle genomes using next-generation sequencing
- (2012) D. M. Bickhart et al. GENOME RESEARCH
- Tabix: fast retrieval of sequence features from generic TAB-delimited files
- (2011) H. Li BIOINFORMATICS
- The variant call format and VCFtools
- (2011) P. Danecek et al. BIOINFORMATICS
- A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
- (2011) H. Li BIOINFORMATICS
- A framework for variation discovery and genotyping using next-generation DNA sequencing data
- (2011) Mark A DePristo et al. NATURE GENETICS
- GCTA: A Tool for Genome-wide Complex Trait Analysis
- (2010) Jian Yang et al. AMERICAN JOURNAL OF HUMAN GENETICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- The European Nucleotide Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
- (2009) Jacob F. Degner et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Analysis of recent segmental duplications in the bovine genome
- (2009) George E Liu et al. BMC GENOMICS
- Unlocking the bovine genome
- (2009) Ross L Tellam et al. BMC GENOMICS
- The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
- (2009) et al. SCIENCE
- Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds
- (2009) et al. SCIENCE
- Real-Time DNA Sequencing from Single Polymerase Molecules
- (2008) J. Eid et al. SCIENCE
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search