Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
Reads0
Chats0
TLDR
The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.Abstract:
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.read more
Citations
More filters
Journal ArticleDOI
Using relatedness networks to infer contemporary dispersal: Application to the endangered mammal Galemys pyrenaicus.
TL;DR: Analyzing relatedness between individuals from different localities and using next‐generation sequencing to infer whether dispersal occurred in recent generations of Pyrenean desman shows that relatedness information can be crucial to understand the contemporary dispersal patterns and conservation status of specific populations of endangered species.
Journal ArticleDOI
The effects of diadromy and its loss on genomic divergence: The case of amphidromous Galaxias maculatus populations.
TL;DR: The genetic diversity and divergence among 20 estuarine and resident populations across the Chilean distribution of G. maculatus was examined and the extent to which selection is involved in the differentiation among resident populations was assessed.
Journal ArticleDOI
Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23.
Khanam Taslima,Khanam Taslima,Stefanie Wehner,John B. Taggart,Hugues de Verdal,Hugues de Verdal,John A. H. Benzie,John A. H. Benzie,Michaël Bekaert,Brendan McAndrew,David J. Penman +10 more
TL;DR: Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23, which will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
Journal ArticleDOI
Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans.
TL;DR: The results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies.
Journal ArticleDOI
Sky, sea, and forest islands: diversification in the African leaf‐folding frog Afrixalus paradorsalis (Anura: Hyperoliidae) of the Lower Guineo‐Congolian rain forest
Kristin L. Charles,Rayna C. Bell,Rayna C. Bell,David C. Blackburn,Marius Burger,Matthew K. Fujita,Václav Gvoždík,Václav Gvoždík,Gregory F.M. Jongsma,Marcel T. Kouete,Adam D. Leaché,Daniel M. Portik,Daniel M. Portik +12 more
TL;DR: To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frog Afrixalus paradorsalis, the role of adjacent land bridge and sky‐islands in diversification is examined.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.