Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics
| Autor: | Nicolas C. Rochette, Angel G. Rivera-Colón, Julian M. Catchen |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine Genotype Locus (genetics) Computational biology Biology 010603 evolutionary biology 01 natural sciences Polymorphism Single Nucleotide De Bruijn graph Population genomics 03 medical and health sciences symbols.namesake Software Genetics Humans Genotyping Ecology Evolution Behavior and Systematics Paired-end tag Contig business.industry High-Throughput Nucleotide Sequencing Bayes Theorem Sequence Analysis DNA 030104 developmental biology Genetics Population Phenotype symbols Metagenomics Precision and recall business Algorithms |
| Zdroj: | Molecular ecologyREFERENCES. 28(21) |
| ISSN: | 1365-294X |
| Popis: | For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively-parallel, short-read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here, we describe the first software natively capable of using paired-end sequencing to derive short contigs from de novo RAD data. Stacks version 2 employs a de Bruijn graph assembler to build and connect contigs from forward and reverse reads for each de novo RAD locus, which it then uses as a reference for read alignments. The new architecture allows all the individuals in a metapopulation to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes, generating RAD loci that are 400-800 bp in length. To prove its recall and precision, we tested the software with simulated data and compared reference-aligned and de novo analyses of three empirical data sets. Our study shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired-end de novo data sets. |
| Databáze: | OpenAIRE |
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