Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences

Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. We report here the algorithms implemented in Stacks and demonstrate their 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.

• Publication year

  2011

• Venue

  G3: Genes, Genomes, Genetics

• Publication date

  2011-08-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1534/g3.111.000240PMID 22384329PMCID 3276136
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• SNP DISCOVERY: NEXT GENERATION SEQUENCING Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

  2011cited by this paper
• Ancestral polyploidy in seed plants and angiosperms

  2011cited by this paper
• Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

  2011cited by this paper
• Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

  2011influential reference
• Resolving postglacial phylogeography using high-throughput sequencing

  2010cited by this paper
• Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

  2010influential reference
• Personal genome sequencing: current approaches and challenges.

  2010cited by this paper
• Quake: quality-aware detection and correction of sequencing errors

  2010cited by this paper
• Phenotypic connections in surprising places

  2010cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• A high density linkage map of the bovine genome

  2009cited by this paper
• A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

  2008cited by this paper
• Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

  2008cited by this paper
• Mapping and quantifying mammalian transcriptomes by RNA-Seq

  2008influential reference
• Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

  2008cited by this paper
• Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.

  2007cited by this paper
• A Linkage Map Reveals a Complex Basis for Segregation Distortion in an Interpopulation Cross in the Moss Ceratodon purpureus

  2007cited by this paper
• An ultradense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers

  2007cited by this paper
• JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations

  2006influential reference
• Assignment of zebrafish genetic linkage groups to chromosomes

  2006cited by this paper
• Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map

  2006cited by this paper
• Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate

  2005cited by this paper
• The zebrafish gene map defines ancestral vertebrate chromosomes.

  2005influential reference
• Local homology recognition and distance measures in linear time using compressed amino acid alphabets.

  2004influential reference
• R/qtl: QTL Mapping in Experimental Crosses

  2003cited by this paper
• Alignment-free sequence comparison-a review

  2003influential reference
• A comparative map of the zebrafish genome.

  2000cited by this paper
• Genetic linkage mapping of zebrafish genes and ESTs.

  2000influential reference
• Zebrafish genetic map with 2000 microsatellite markers.

  1999cited by this paper
• Assessment of polymorphism in zebrafish mapping strains.

  1999cited by this paper
• Base-calling of automated sequencer traces using phred. II. Error probabilities.

  1998cited by this paper
• Zebrafish hox clusters and vertebrate genome evolution.

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997influential reference
• Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout.

  1997cited by this paper
• A genetic linkage map for the zebrafish.

  1994cited by this paper
• Segregation analyses and gene-centromere distances in zebrafish.

  1986cited by this paper
• Literature cited

  1924cited by this paper
• THE LINEAR ARRANGEMENT OF SIX SEX-LINKED FACTORS IN DROSOPHILA, AS SHOWN BY THEIR MODE OF ASSOCIATION

  1913cited by this paper

• When high dispersal meets high diversification: the case of the White-bellied Cuckooshrike, Coracina papuensis

  2026influential citation
• Integrative phylogenetics and geography unveil Quaternary diversification and mitochondrial-nuclear discordance in Odorrana schmackeri sensu lato (Anura, Ranidae): Roles of Qinghai-Tibetan uplift, climate oscillations, and asymmetric gene flow.

  2026cites this paper
• The presence of a marker associated with Pacific oyster resistance to OsHV-1 does not affect susceptibility to Vibrio aestuarianus

  2026influential citation
• Genomic Architecture of Inbreeding Depression Associated With Hatching Failure in an Endangered Parrot

  2026cites this paper
• A cryptic hybrid zone reveals the genomic basis of flower colour variation in a plant with a large and complex genome

  2026cites this paper
• Cave evolution on repeat: reuse of the same genomic regions across lineages but not across traits in Astyanax mexicanus

  2026cites this paper
• Genetic basis of cuticular hydrocarbon variation in the desert ant Cataglyphis niger

  2026cites this paper
• Evidence for Cascading Host‐Associated Differentiation in Insect Gall Trophic Networks

  2026cites this paper
• Leveraging Knowledge of Traditional Italian Maize Landrace Diversity to Identify Signals of Local Adaptation

  2026cites this paper
• Quantitative Trait Loci Associated With Durable Resistance to Stripe Rust in Winter Wheat

  2026influential citation
• The critically endangered Dipterocarpus cinereus is undergoing a genetic bottleneck: evidence from MIG-seq analysis

  2026influential citation
• Invasion processes of apomictic hybrids between introduced (Taraxacum officinale) and native dandelions in Japan: stage-specific roles of hybridization and ploidy levels

  2026cites this paper
• Invasive patterns of Biomphalaria straminea revealed by genetic mapping in the Greater Bay Area, China

  2026cites this paper
• Learning About the Role of Rivers in the Distribution of Genetic Diversity of a Neotropical Primate

  2026influential citation
• Genotyping-by-Sequencing Reveals Low Genetic Diversity and Pronounced Geographic Structuring in the Endangered Medicinal Plant Coptis chinensis var. brevisepala

  2026influential citation
• Genetic analysis of wild walnuts in Xinjiang based on whole-genome resequencing

  2025cites this paper
• Spatiotemporal variation in abundance and genetic structure in an urban–rural landscape: Aedes albopictus (Skuse, 1894) (Diptera: Culicidae) in Wake County, NC

  2025cites this paper
• Development of genomic resources to support population assessment and breeding strategies in the dusky grouper (Epinephelus marginatus)

  2025cites this paper
• Identification of Male-Specific Markers by Genotyping-by-Sequencing in the Giant Spiny Frog, Quasipaa spinosa

  2025cites this paper
• Spontaneous mutant in threespine stickleback connects endosome trafficking disorders and inflammatory bowel diseases via changes in the gut microbiome

  2025cites this paper
• Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program

  2025cites this paper
• Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus)

  2025cites this paper
• Selection maintains floral color polymorphism in scarlet paintbrush, Castilleja coccinea, reflecting combined ecological factors.

  2025cites this paper
• Two mutations in the same MYC-bHLH transcription factor cause segregation of purple coloration of stolons and seed heads in Zoysia japonica × Zoysia matrella F2 and F1 populations

  2025influential citation
• Historical Impacts of Invasive Species May Not Always Be What They Seem: A Genetic Perspective From an Endangered Native Species

  2025cites this paper
• Genetic evidence reveals that two wild boar (Sus scrofa) lineages invaded an island in Japan by swimming

  2025influential citation
• Genetic insights into the invasion success of a non-native weed: the case of stinking passionflower (Passiflora foetida sens. lat.) in Australia

  2025cites this paper
• Is A critically endangered Vatica bantamensis Burck (Dipterocarpaceae) endemic to West Java, Indonesia experiencing a genetic bottleneck?

  2025influential citation
• An alpine plant shows no decrease in genetic diversity associated with rapid post‐glacial range expansion

  2025cites this paper
• Genomic diversity and population structure of Oenocarpus minor in the Brazilian Amazon: implications for conservation

  2025cites this paper
• Genetic Analysis of Recently Discovered Least Chub Populations in the Upper Snake River and Bonneville Drainages

  2025cites this paper
• Population genomics of rainforest mountain frogs (Anura: Limnodynastidae: Philoria) severely impacted by the Australian megafires

  2025influential citation
• Sympatry and evolution: relationships between the endemic Myrcia guarujana and the widely distributed M. spectabilis.

  2025cites this paper
• Spatiotemporal variation in abundance and genetic structure across the urban-rural landscape gradient: Aedes albopictus (Skuse, 1894) (Diptera: Culicidae) in Wake County, NC

  2025influential citation
• A genomic perspective on adaptation to heterogeneous environments for Cycas segmentifida (Cycadaceae), an endemic cycad in southwest China.

  2025cites this paper
• Conservation Genomics for Threatened New Zealand Gentianella calcis (Gentianaceae) and Implications for Vulnerable Limestone Ecosystems

  2025influential citation
• Landscape genomics of the contact zone between the Mexican red oaks Quercus affinis and Quercus laurina: genetic diversity, hybridization and local adaptation

  2025cites this paper
• Biobanks in GENETICS and G3: tackling the statistical challenges

  2025cites this paper
• Exploring the Genetic Basis of Wild Boar (Sus scrofa) and Its Connection to Classical Swine Fever Spread

  2025influential citation
• Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition

  2025cites this paper
• Molecular and morphological data support the synonymy of Muricanthusradix Gmelin, 1791 and Muricanthusambiguus Reeve, 1845 (Gastropoda, Muricidae)

  2025influential citation
• Population genetic structure of 2 mole species (Mogera imaizumii and M. wogura) in the Japanese Archipelago

  2025influential citation
• Surveying Selection Signatures in Murrah Buffalo Using Genome-Wide SNP Data

  2025cites this paper
• Genomic insights into the reticulate evolution of viviparous Phrynocephalus lizards on the Qinghai-Tibetan Plateau.

  2025cites this paper
• A single nucleotide polymorphism panel for identifying North American species and hybrids in the genus Morone

  2025cites this paper
• Sex Differentiation and Long‐Distance Gene Flow in the Elusive Antarctic Fish Aethotaxis mitopteryx

  2025influential citation
• Genetic structure and local adaptation of Nitraria sphaerocarpa populations from arid northwestern China

  2025cites this paper
• Spatiotemporal Population Genomics of the Invasive Whitefly Bemisia tabaci MED in China: Implications for Surveillance and Sustainable Control

  2025cites this paper
• Release of marketed individuals increases the risk of genetic disturbance in the pet insect Trypoxylus dichotomus

  2025cites this paper
• Fish Show Genetic Evolutionary Responses to River Regulation

  2025cites this paper
• Population genomics highlight the vulnerability of coral-dwelling gobies to ecological losses due to climatic disturbances

  2025cites this paper
• Population structure and divergence time among East Greenland and West Greenland/Eastern Canadian Arctic narwhals, Monodon monoceros

  2025influential citation
• Preclinical models for autism spectrum disorder: past, present, and future.

  2025cites this paper
• What Is the Population Structure of Poecilogonic Species? Evidence From Large‐Scale Genotyping in a Neogastropod Lineage (Conoidea: Raphitoma)

  2025cites this paper
• Human‐Mediated Dispersal Routes Structure Sahara Mustard Genomics

  2025cites this paper
• Genetic parallelism underlying repeated bill divergence in the Island Scrub-jay (Aphelocoma insularis) increases at higher genetic levels of organization.

  2025cites this paper
• Conservation genomics of the imperiled Leon springs pupfish, Cyprinodon bovinus, across temporal and spatial scales

  2025cites this paper
• Using machine learning for the discovery of epistatic fruit rot resistance markers

  2025cites this paper
• Apomixis in Farmers’ Fields: Overview, Case Studies from Forage Grasses and Considerations for Future Apomictic Crops

  2025cites this paper
• Phylogeographic analyses detect population structure and limited gene flow in the Peacock Grouper Cephalopholis argus across Micronesia

  2025cites this paper
• Genome-wide SNP diversity in natural and cultivated populations informs restoration ecology with three Calamagrostis species from the Northwest Territories of Canada

  2025influential citation
• TWO STEPS AWAY FROM EXTINCTION: DO YOU BELIEVE?

  2025influential citation
• Early signals of fragmentation of flat-tailed horned lizards in the Yuma Desert

  2025influential citation
• Biobanks in GENETICS and G3: tackling the statistical challenges

  2025cites this paper
• Population Genetics Provides Insights Into the Impact of Future Climate Change on the Genetic Structure and Distribution of Asian Warty Newts (Genus Paramesotriton)

  2025cites this paper
• Genome-wide scan for SNPs and selective sweeps reveals candidate genes and QTLs for milk production and reproduction traits in Indian Kankrej cattle

  2025cites this paper
• Landscape connectivity and genetic structure of animal populations in urban ponds

  2025influential citation
• Recent Divergence and Microgeographic Genetic Structure in an Endangered Australian Songbird: The Southern Black‐Throated Finch

  2025cites this paper
• Genetic Admixture and Novel Host Shifts in a Parasitic Plant, Orobanche boninsimae (Orobanchaceae), Endemic to the Ogasawara Islands

  2025influential citation
• Evaluation of the conservation value and conservation difficulty of local populations of the rare plant Viola raddeana based on genetic diversity and gene expression information using next‐generation sequencers

  2025influential citation
• Landscape transcriptomic analysis detects thermal stress responses and potential adaptive variation in wild brook trout (Salvelinus fontinalis) during successive heatwaves.

  2025cites this paper
• Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

  2025cites this paper
• The Intertidal North‐South Split: Oceanographic Features and Life History Shape the Phylogeography of Chiton Acanthochitona rubrolineata

  2025cites this paper
• Genomic Insights From Natural History Collections Reveal Cryptic Speciation in Coral Guard Crabs (Family: Trapeziidae)

  2025cites this paper
• Murky mysteries: population structure and gene flow of the estuarine darter goby (Ctenogobius boleosoma)

  2025cites this paper
• Population stratification in Northern shrimp (Pandalus borealis) off Iceland evident from RADseq analysis

  2025cites this paper
• Population structure of the Chub mackerel Scomber japonicus, in waters of the northwest of Mexico

  2025cites this paper
• Population genomics of Gymnogeophagus labiatus and G. lacustris reinforces the role of hydrographic isolation between evolutionary lineages (Cichlidae: Geophagini)

  2025cites this paper
• Population Genomic Assessment of Dudleya brevifolia for in situ Conservation Management.

  2025cites this paper
• The evolution of genomic organization through chromosomal rearrangements in Arctic charr (Salvelinus alpinus).

  2025cites this paper
• The origins and spread of the opium poppy (Papaver somniferum L.) revealed by genomics and seed morphometrics

  2025cites this paper
• COI barcoding can distinguish bisexual and parthenogenetic populations of Haemaphysalis longicornis in Japan: Revisiting methods with SNP analysis as another possible method

  2025cites this paper
• Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses

  2025influential citation
• Do morphologically defined groups correspond to reproductively isolated species? A case study in Myrmica ants from Switzerland

  2025cites this paper
• Harpy: a pipeline for processing haplotagging linked-read data

  2025cites this paper
• High residual additive genetic variability in a Pacific blue shrimp Litopenaeus stylirostris population after 36 generations of domestication from only 4 estimated founders

  2025cites this paper
• Genetic Monitoring of Wild and Captive Populations of Barrens Topminnow (Fundulus Julisia)

  2025cites this paper
• The roles of divergent and parallel selection in Amazonian and Andean bird responses to glacial cycles

  2025influential citation
• Assessing Genetic Variation in Guadua angustifolia Through RAD-Seq Analysis

  2025influential citation
• Changes in biodiversity drive trypanosome infections of wildlife in Panama

  2025cites this paper
• Clarifying genetic relationships and intraspecific variation of lentic-breeding Japanese salamanders (Amphibia, Caudata, Hynobiidae) based on mitochondrial DNA and genome-wide SNP

  2025cites this paper
• Comparative Phylogeography of West African Rainforest Frogs Reveals Regional Variation in Refugia Dynamics

  2025cites this paper
• Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds

  2025cites this paper
• Genomic analysis highlights the conservation significance of Torenia concolor (Linderniaceae) from the periphery of its distribution range

  2025influential citation
• Genomic insights into genetic diversity and seed coat color change in common bean composite populations

  2025cites this paper
• Are We Witnessing a Speciation Continuum? Evidence From Current and Past Gene Flow in the Genus Oritrophium s.s. (Asteraceae) From the Tropical High Andes

  2025influential citation
• Rapid establishment of species barriers in plants compared with that in animals.

  2025cites this paper
• Genomic differentiation between wild Caspian Sea and Iranian farmed common carp (Cyprinus carpio) using 2bRAD-seq

  2025cites this paper
• Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map

  2025cites this paper
• Bambara groundnut [Vigna subterranea (L.) Verdc.] genetic diversity and population structure assessed through next‐generation sequencing technologies: Restriction‐site‐associated DNA sequencing

  2025cites this paper