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
The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system.
Kang Du,Kang Du,Sven Wuertz,Mateus Contar Adolfi,Susanne Kneitz,Matthias Stöck,Marcos De Oliveira,Marcos De Oliveira,Rafael Henrique Nóbrega,Jenny Ormanns,Werner Kloas,Romain Feron,Christophe Klopp,Hugues Parrinello,Laurent Journot,Shunping He,John H. Postlethwait,Axel Meyer,Yann Guiguen,Manfred Schartl,Manfred Schartl +20 more
TL;DR: W Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.
Journal ArticleDOI
Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region
Kevin J. Emerson,Jan E. Conn,Jan E. Conn,Eduardo Sterlino Bergo,Melissa A Randel,Maria Anice Mureb Sallum +5 more
TL;DR: It is inferred that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersalbetween the Paranas and Brazilian dominion populations.
Journal ArticleDOI
SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus).
TL;DR: Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift, providing direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.
Journal ArticleDOI
Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua).
Luciano B. Beheregaray,Lauren V. Pfeiffer,Catherine R. M. Attard,Jonathan Sandoval-Castillo,Fabricius M. C. B. Domingos,Leanne K. Faulks,Dean M. Gilligan,Peter J. Unmack +7 more
TL;DR: This work used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia, and identified cases suggestive of anthropogenic hybridization between lineages.
Journal ArticleDOI
A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data.
Kimberly R. Andrews,Jennifer R. Adams,E. Frances Cassirer,Raina K. Plowright,Colby Gardner,Maggie Dwire,Paul A. Hohenlohe,Lisette P. Waits +7 more
TL;DR: A bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site‐associated DNA sequencing (RADseq) data is developed, and analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy.
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.