Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
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Summary
The algorithms implemented in Stacks are reported and demonstrated to be efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio.
- Type
- article
- Published
- 2011-08-01
- Cited by
- 1,972
- References
- 40
- Access
- Open access
- OpenAlex
- https://openalex.org/W2161901637
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:7012264
Keywords
Genotyping, Biology, Reference genome, Genetics, Genome
References
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- A genetic linkage map for the zebrafish.
- A high density linkage map of the bovine genome
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- Ancestral polyploidy in seed plants and angiosperms
- Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication
- Local homology recognition and distance measures in linear time using compressed amino acid alphabets.
- Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads
- A comparative map of the zebrafish genome.
- Personal genome sequencing: current approaches and challenges.
- Zebrafish genetic map with 2000 microsatellite markers.
- A salmonid EST genomic study: genes, duplications, phylogeny and microarrays
- Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate
- Assignment of zebrafish genetic linkage groups to chromosomes
- THE LINEAR ARRANGEMENT OF SIX SEX-LINKED FACTORS IN DROSOPHILA, AS SHOWN BY THEIR MODE OF ASSOCIATION
- Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.
- Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map
- Assessment of polymorphism in zebrafish mapping strains.
- The Sequence Alignment/Map format and SAMtools
Cited by
- Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra
- High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment
- Hybrid dynamics in a species group of swallowtail butterflies
- Genomic islands of divergence linked to ecotypic variation in sockeye salmon
- Adaptive capabilities and fitness consequences associated with pollution exposure in fish
- Deriving genotypes from RAD-seq short-read data using Stacks
- Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel
- Reconstructing the evolutionary history of chromosomal races on islands: a genome-wide analysis of natural house mouse populations.
- The genetic basis of pigment pattern differentiation in Lake Malawi African cichlids
- Phylogenetics and Mating System Evolution in the Southern South American Valeriana (Valerianaceae)
- Genome-wide genetic diversity of rove beetle populations along a metal pollution gradient.
- Evolution of Fish in Extreme Environments : Insights from the Magadi tilapia (Alcolapia grahami)
- Experimental Evolution of Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei
- Sex chromosome evolution of papaya: Dynamic structural and expression changes and identification of associated traits
- Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing
- Exploring the Opportunities for Divergence in Heterogeneous Environmnets in the Tropical Andes.
- Phylogeographic History and Temperature-Mediated Evolution of the Green Anole, Anolis Carolinensis
- A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.
- História evolutiva e dinâmica demográfica de Cavia intermedia (Mammalia: Rodentia) inferida através de abordagem genômica
- Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.
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