SNP4OrphanSpecies: A bio-informatic pipeline to isolate robust molecular markers for phylogeny, phylogeographical and population genetic studies in non-model species.

DOI

This pipeline performs a de-novo genome assembly, identifies single copy genes in the genome, and designs several pools of pair of primers for amplifying regions of these genes in multiplex. The pipeline is implemented in a SnakeMake workflow and uses Illumina data for the de-novo genome assembly. It was tested for Diplodia sapinea, a fungal pathogen causing severe infections in numerous conifers.

Identifier
DOI https://doi.org/10.15454/GWKRKY
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.15454/GWKRKY
Provenance
Creator Penaud, Benjamin; Dutech, Cyril; Laurent, Benoît
Publisher Recherche Data Gouv
Contributor Dutech, Cyril; Penaud, Benjamin
Publication Year 2021
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact Dutech, Cyril (INRA - Institut National de la Recherche Agronomique); Penaud, Benjamin (INRA - Institut National de la Recherche Agronomique)
Representation
Resource Type Dataset
Format application/vnd.oasis.opendocument.text; application/x-xz; application/octet-stream
Size 119790; 97908; 1502838784; 2452505092; 18052; 92200; 65120; 1760; 7133; 46055; 73156
Version 1.0
Discipline Agriculture, Forestry, Horticulture; Computer Science; Geosciences; Life Sciences; Plant Science; Biology; Omics; Microbial Ecology and Applied Microbiology; General Genetics; Silviculture; Agricultural Sciences; Agriculture, Forestry, Horticulture, Aquaculture; Agriculture, Forestry, Horticulture, Aquaculture and Veterinary Medicine; Basic Biological and Medical Research; Biospheric Sciences; Computer Science, Electrical and System Engineering; Earth and Environmental Science; Ecology; Engineering Sciences; Environmental Research; Medicine; Natural Sciences