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
Posted ContentDOI
Fine-scale landscape genomics helps explain the slow spread of Wolbachia through the Aedes aegypti population in Cairns, Australia
TL;DR: The landscape genomics approach can be extended to other host/symbiont systems that are being considered for biocontrol, and found a pair of full-siblings of different infection status, suggesting loss of Wolbachia in the field.
Journal ArticleDOI
Residual survival and local dispersal drive reinfestation by Triatoma dimidiata following insecticide application in Guatemala.
Sara Helms Cahan,Lucia C. Orantes,Kimberly F. Wallin,Kimberly F. Wallin,John P. Hanley,Donna M. Rizzo,Lori Stevens,Patricia L. Dorn,Antonieta Rodas,Carlota Monroy +9 more
TL;DR: It is concluded that house structural improvements, an integral part of the Ecohealth approach that makes houses refractory to vector colonization and persistence, are critical for long-term reduction of T. dimidiata infestation.
Posted ContentDOI
Spatial population genomics of a recent mosquito invasion
Thomas L Schmidt,Tom Swan,Tom Swan,Jessica Chung,Stephan Karl,Stephan Karl,Samuel Demok,Qiong Yang,Matthew A. Field,Matthew A. Field,Mutizwa Odwell Muzari,Gerhard Ehlers,Mathew Brugh,Rodney Bellwood,Peter Horne,Thomas R. Burkot,Scott A. Ritchie,Scott A. Ritchie,Ary A. Hoffmann +18 more
TL;DR: By treating dispersal as both an intergenerational process and a set of discrete events, this work describes a highly interconnected invasive system in a 2004 invasion of Aedes albopictus in the Torres Strait Islands of Australia.
Journal ArticleDOI
Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon.
Jianhua Xiao,Jianhua Xiao,Xin Ding,Lang Li,Lang Li,Hui Ma,Xiuqin Ci,Xiuqin Ci,Marlien van der Merwe,John G. Conran,Jie Li,Jie Li +11 more
TL;DR: It is suggested that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape‐level patterns of genetic diversity within P. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants.
Journal ArticleDOI
Identification of sex-specific sequences through 2b-RAD sequencing in Pseudobagrus ussuriensis
Chuankun Zhu,Haiyang Liu,Lei Cheng,Pan Zhengjun,Guoliang Chang,Nan Wu,Hui Wang,Ding Huaiyu,Ying Fang,Long Wang +9 more
TL;DR: Reduced restriction site-associated DNA sequencing was performed in five female and five male P. ussuriensis using the 2b-RAD approach to identify sex-specific sequences, indicating three male-specific markers and seven male- specific sequences, which were further confirmed in 300 individuals from two full-sib families and showed the expected 1:1 sex ratio.
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.