Related references
Note: Only part of the references are listed.A chromosome-level reference genome and pangenome for barn swallow population genomics
Simona Secomandi et al.
CELL REPORTS (2023)
Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs
Yi-Fan Jiang et al.
ISCIENCE (2023)
A draft human pangenome reference
Wen-Wei Liao et al.
NATURE (2023)
Pangenome graph construction from genome alignments with Minigraph-Cactus
Glenn Hickey et al.
NATURE BIOTECHNOLOGY (2023)
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Mikko Rautiainen et al.
NATURE BIOTECHNOLOGY (2023)
Evolutionary analysis of a complete chicken genome
Zhen Huang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)
The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus
Wesley C. Warren et al.
SCIENTIFIC REPORTS (2023)
Fourth Report on Chicken Genes and Chromosomes 2022
Jacqueline Smith et al.
CYTOGENETIC AND GENOME RESEARCH (2023)
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Alexander S. Leonard et al.
GENOME BIOLOGY (2023)
Unbiased pangenome graphs
Erik Garrison et al.
BIOINFORMATICS (2023)
Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Yury A. Barbitoff et al.
BMC GENOMICS (2022)
ODGI: understanding pangenome graphs
Andrea Guarracino et al.
BIOINFORMATICS (2022)
De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions
Ming Li et al.
MOLECULAR BIOLOGY AND EVOLUTION (2022)
Haplotype-resolved assembly of diploid genomes without parental data
Haoyu Cheng et al.
NATURE BIOTECHNOLOGY (2022)
The complete sequence of a human genome
Sergey Nurk et al.
SCIENCE (2022)
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
Erik Garrison et al.
PLOS COMPUTATIONAL BIOLOGY (2022)
GBZ file format for pangenome graphs
Jouni Siren et al.
BIOINFORMATICS (2022)
Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
Yang Zhou et al.
GENOME RESEARCH (2022)
Deadly bird flu establishes a foothold in North America
Erik Stokstad
SCIENCE (2022)
Comprehensive analysis of structural variants in chickens using PacBio sequencing
Jinxin Zhang et al.
FRONTIERS IN GENETICS (2022)
Widespread false gene gains caused by duplication errors in genome assemblies
Byung June Ko et al.
GENOME BIOLOGY (2022)
Fast gap-affine pairwise alignment using the wavefront algorithm
Santiago Marco-Sola et al.
BIOINFORMATICS (2021)
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Caroline Belser et al.
COMMUNICATIONS BIOLOGY (2021)
Identification of new genes and quantitative trait locis associated with growth curve parameters in F2 chicken population using genome-wide association study
R. Seifi Moroudi et al.
ANIMAL GENETICS (2021)
Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations
N. Dementieva et al.
ANIMAL (2021)
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Haoyu Cheng et al.
NATURE METHODS (2021)
Multithreaded variant calling in elPrep 5
Charlotte Herzeel et al.
PLOS ONE (2021)
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Jouni Siren et al.
SCIENCE (2021)
The impact of endogenous Avian Leukosis Viruses (ALVE) on production traits in elite layer lines
Janet E. Fulton et al.
POULTRY SCIENCE (2021)
Twelve years of SAMtools and BCFtools
Petr Danecek et al.
GIGASCIENCE (2021)
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies
Xuefang Zhao et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2021)
Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
Aleksandra Bliznina et al.
BMC GENOMICS (2021)
Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection
Albert Perlas et al.
FRONTIERS IN IMMUNOLOGY (2021)
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie et al.
NATURE (2021)
The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size
Kejun Wang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
Towards population-scale long-read sequencing
Wouter De Coster et al.
NATURE REVIEWS GENETICS (2021)
Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Lingzhan Xue et al.
GENOME BIOLOGY (2021)
Identifying and removing haplotypic duplication in primary genome assemblies
Dengfeng Guan et al.
BIOINFORMATICS (2020)
Pangenome Graphs
Jordan M. Eizenga et al.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 21, 2020 (2020)
Whole-genome resequencing of Dulong Chicken reveal signatures of selection
Q. Wang et al.
BRITISH POULTRY SCIENCE (2020)
The design and construction of reference pangenome graphs with minigraph
Heng Li et al.
GENOME BIOLOGY (2020)
Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens
Andrew S. Mason et al.
GENETICS SELECTION EVOLUTION (2020)
Genotyping structural variants in pangenome graphs using the vg toolkit
Glenn Hickey et al.
GENOME BIOLOGY (2020)
Population genomics identifies patterns of genetic diversity and selection in chicken
Diyan Li et al.
BMC GENOMICS (2019)
The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution
Dorcus Kholofelo Malomane et al.
BMC GENOMICS (2019)
A new chicken 55K SNP genotyping array
Ranran Liu et al.
BMC GENOMICS (2019)
The presence and impact of reference bias on population genomic studies of prehistoric human populations
Torsten Gunther et al.
PLOS GENETICS (2019)
Characterizing the Major Structural Variant Alleles of the Human Genome
Peter A. Audano et al.
CELL (2019)
Structural variant calling: the long and the short of it
Medhat Mahmoud et al.
GENOME BIOLOGY (2019)
Paragraph: a graph-based structural variant genotyper for short-read sequence data
Sai Chen et al.
GENOME BIOLOGY (2019)
Endogenous viral gene ev21 is not responsible for the expression of late feathering in chickens
A. Takenouchi et al.
POULTRY SCIENCE (2018)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
Analysis of a genetic factors contributing to feathering phenotype in chickens
Xiuling Zhang et al.
POULTRY SCIENCE (2018)
A fast adaptive algorithm for computing whole-genome homology maps
Chirag Jain et al.
BIOINFORMATICS (2018)
Variation graph toolkit improves read mapping by representing genetic variation in the reference
Erik Garrison et al.
NATURE BIOTECHNOLOGY (2018)
A universal SNP and small-indel variant caller using deep neural networks
Ryan Poplin et al.
NATURE BIOTECHNOLOGY (2018)
Systematic evaluation of error rates and causes in short samples in next-generation sequencing
Franziska Pfeiffer et al.
SCIENTIFIC REPORTS (2018)
Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek's disease
Lingyang Xu et al.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY (2018)
Identifying the genetic basis for resistance to avian influenza in commercial egg layer chickens
W. Drobik-Czwarno et al.
ANIMAL (2018)
Expression patterns of endogenous avian retrovirus ALVE1 and its response to infection with exogenous avian tumour viruses
Xuming Hu et al.
ARCHIVES OF VIROLOGY (2017)
Scaffolding of long read assemblies using long range contact information
Jay Ghurye et al.
BMC GENOMICS (2017)
gEVAL-a web-based browser for evaluating genome assemblies
William Chow et al.
BIOINFORMATICS (2016)
Copy number variation identification and analysis of the chicken genome using a 60K SNP BeadChip
Y. S. Rao et al.
POULTRY SCIENCE (2016)
Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.
Ryan R. Wick et al.
BIOINFORMATICS (2015)
Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data
Debora Y. C. Brandt et al.
G3-GENES GENOMES GENETICS (2015)
Second-generation PLINK: rising to the challenge of larger and richer datasets
Christopher C. Chang et al.
GIGASCIENCE (2015)
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch et al.
BIOINFORMATICS (2012)
Genotype and SNP calling from next-generation sequencing data
Rasmus Nielsen et al.
NATURE REVIEWS GENETICS (2011)
Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken
Martin G. Elferink et al.
BMC GENOMICS (2008)
Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens
CM Chang et al.
BMC GENOMICS (2006)