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
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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
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How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish.
Carly F. Graham,Douglas R. Boreham,Richard G. Manzon,Wendylee Stott,Joanna Y. Wilson,Christopher M. Somers +5 more
TL;DR: It is shown that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision and that early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies.
Journal ArticleDOI
Conservation genomics identifies impact of trade in a threatened songbird
Elize Y. X. Ng,Kritika M. Garg,Gabriel W. Low,Balaji Chattopadhyay,Rachel Rui Ying Oh,Jessica G. H. Lee,Frank E. Rheindt +6 more
TL;DR: In this paper, the white-rumped shama (Copsychus malabaricus) was found to have high genomic uniformity across its mainland Southeast Asian range, indicating that future reintroductions of birds from regions with less poaching could help bolster populations in regions with intense poaching pressure.
Journal ArticleDOI
Characterization of limes (Citrus aurantifolia) grown in Bhutan and Indonesia using high-throughput sequencing
TL;DR: In this paper, the authors characterized and compared limes grown in Bhutan (n = 5 accessions) and Indonesia(n = 3 accessions), and the limes were separated into two groups based on their morphology.
Journal ArticleDOI
Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel.
Robin Cristofari,Paula Plaza,Claudia E. Fernández,Emiliano Trucchi,Emiliano Trucchi,Nicolas Gouin,Céline Le Bohec,Carlos B. Zavalaga,Joanna Alfaro-Shigueto,Guillermo Luna-Jorquera +9 more
TL;DR: The range-wide population structure of the Peruvian diving petrel is explored, and it is shown that this small seabird exhibits extreme philopatric behavior at the island level, which underline the importance of considering the philop atric behavior and demographic independence of breeding populations, even at very fine spatial scales, in spatial planning for marine coastal areas.
Journal ArticleDOI
Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation
Sean J Buckley,Fabricius M. C. B. Domingos,Fabricius M. C. B. Domingos,Catherine R. M. Attard,Chris J. Brauer,Jonathan Sandoval-Castillo,Ryan Lodge,Peter J. Unmack,Luciano B. Beheregaray +8 more
TL;DR: The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent and proposing three cryptic species within a southwestern species complex.
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.