3/31/2023 0 Comments Pdf stacks and box(F) The cstacks program loads stacks from the parents of a genetic cross into a Catalog to create a set of all possible loci in a mapping cross. (E) ustacks calls a consensus sequence and records SNP and haplotype data. An SNP model in ustacks checks each locus at each nucleotide position for polymorphisms. (D) ustacks matches secondary reads that were not initially placed in a stack against putative loci to increase stack depth. (C) ustacks merges matched stacks to form putative loci. The ustacks program breaks down each stack again into k-mers and queries the k-mer Dictionary to create a list of potentially matching stacks, which can be visualized as nodes in a graph connected by the nucleotide distance between them. (B) The ustacks program breaks down the sequence of each stack into k-mers and loads them into a dictionary. (A) The ustacks program forms stacks in an individual from short sequencing reads (cleaned by process_) that match exactly. We report here the algorithms implemented in Stacks and demonstrate their efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio. Stacks can generate markers for ultra-dense genetic linkage maps, facilitate the examination of population phylogeography, and help in reference genome assembly. From reduced representation Illumina sequence data, such as RAD-tags, Stacks can recover thousands of single nucleotide polymorphism (SNP) markers useful for the genetic analysis of crosses or populations. Stacks is a software system that uses short-read sequence data to identify and genotype loci in a set of individuals either de novo or by comparison to a reference genome. Advances in sequencing technology provide special opportunities for genotyping individuals with speed and thrift, but the lack of software to automate the calling of tens of thousands of genotypes over hundreds of individuals has hindered progress.
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