Idioma:

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Rochette, Nicolas C. ; Rivera‐Colón, Angel G. ; Catchen, Julian M.

Molecular ecology, 2019-11, Vol.28 (21), p.4737-4754 [Periódico revisado por pares]

England: Blackwell Publishing Ltd

Texto completo disponível

Citações Citado por

Enviar para

Título:
Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics
Autor: Rochette, Nicolas C. ; Rivera‐Colón, Angel G. ; Catchen, Julian M.
Assuntos: Algorithms ; Analytical methods ; Bayesian analysis ; bioinformatics ; Computer programs ; Computer simulation ; conservation genetics ; Datasets ; Empirical analysis ; Genetics ; genotype calling ; Genotypes ; Genotyping ; Graph theory ; haplotype phasing ; Haplotypes ; Loci ; Metapopulations ; Population genetics ; Population studies ; restriction‐site associated DNA sequencing ; Single-nucleotide polymorphism ; Software ; Stacks
É parte de: Molecular ecology, 2019-11, Vol.28 (21), p.4737-4754
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descrição: 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.
Editor: England: Blackwell Publishing Ltd
Idioma: Inglês

Links

View this record in MEDLINE/PubMed

Voltar para lista de resultados

Realização: Logos de Redes Sociais:

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Rochette, Nicolas C. ; Rivera‐Colón, Angel G. ; Catchen, Julian M.

England: Blackwell Publishing Ltd

Buscando em bases de dados remotas. Favor aguardar.