- Home
- Publications
- Publication Search
- Publication Details
Title
Deriving genotypes from RAD-seq short-read data using Stacks
Authors
Keywords
-
Journal
Nature Protocols
Volume 12, Issue 12, Pages 2640-2659
Publisher
Springer Nature
Online
2017-12-01
DOI
10.1038/nprot.2017.123
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
- (2017) Paolo Franchini et al. MOLECULAR ECOLOGY
- Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
- (2016) Naiara Rodríguez-Ezpeleta et al. Molecular Ecology Resources
- The Atlantic salmon genome provides insights into rediploidization
- (2016) Sigbjørn Lien et al. NATURE
- Harnessing the power of RADseq for ecological and evolutionary genomics
- (2016) Kimberly R. Andrews et al. NATURE REVIEWS GENETICS
- Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids
- (2016) Andreas F. Kautt et al. PLoS Genetics
- Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens
- (2016) Tomasz Suchan et al. PLoS One
- RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping
- (2015) O. A. Ali et al. GENETICS
- AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data
- (2015) Michael G. Sovic et al. Molecular Ecology Resources
- Evolution of stickleback in 50 years on earthquake-uplifted islands
- (2015) Emily A. Lescak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
- (2015) M. Malinsky et al. SCIENCE
- Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species
- (2015) Michael G. Harvey et al. PeerJ
- PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
- (2014) Deren A. R. Eaton BIOINFORMATICS
- ANGSD: Analysis of Next Generation Sequencing Data
- (2014) Thorfinn Sand Korneliussen et al. BMC BIOINFORMATICS
- A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo
- (2014) Ingo Braasch et al. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION
- Comparative population genomics in animals uncovers the determinants of genetic diversity
- (2014) J. Romiguier et al. NATURE
- TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
- (2014) Jeffrey C. Glaubitz et al. PLoS One
- dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
- (2014) Jonathan B. Puritz et al. PeerJ
- The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing
- (2013) Julian Catchen et al. MOLECULAR ECOLOGY
- Genotyping-by-sequencing in ecological and conservation genomics
- (2013) Shawn R. Narum et al. MOLECULAR ECOLOGY
- Stacks: an analysis tool set for population genomics
- (2013) Julian Catchen et al. MOLECULAR ECOLOGY
- Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
- (2013) Fei Lu et al. PLoS Genetics
- ezRAD: a simplified method for genomic genotyping in non-model organisms
- (2013) Robert J. Toonen et al. PeerJ
- Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
- (2012) Z. Chong et al. BIOINFORMATICS
- Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
- (2012) Brant K. Peterson et al. PLoS One
- adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
- (2011) Thibaut Jombart 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
- Haplotype phasing: existing methods and new developments
- (2011) Sharon R. Browning et al. NATURE REVIEWS GENETICS
- Genotype and SNP calling from next-generation sequencing data
- (2011) Rasmus Nielsen et al. NATURE REVIEWS GENETICS
- A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
- (2011) Robert J. Elshire et al. PLoS One
- Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences
- (2011) Julian M. Catchen et al. G3-Genes Genomes Genetics
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
- (2010) Paul A. Hohenlohe et al. PLoS Genetics
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
- (2008) Nathan A. Baird et al. PLoS One
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now