Utilize este identificador para referenciar este registo: http://hdl.handle.net/10400.7/347
Título: Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms
Autor: Greminger, Maja P
Stölting, Kai N
Nater, Alexander
Goossens, Benoit
Arora, Natasha
Bruggmann, Rémy
Patrignani, Andrea
Nussberger, Beatrice
Sharma, Reeta
Kraus, Robert H S
Ambu, Laurentius N
Singleton, Ian
Chikhi, Lounes
van Schaik, Carel P
Krützen, Michael
Palavras-chave: Next-generation sequencing
Single-nucleotide polymorphisms
Reduced-representation libraries
Bioinformatics
GATK
SAMtools
CLC genomics workbench
Great apes
Data: 10-Jan-2014
Editora: BioMed Central
Citação: Greminger et al. : Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct compariso ns of SNP calling algorithms. BMC Genomics 2014 15 :16.
Resumo: High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequencing. Like similar approaches, RRL sequencing reduces ascertainment bias due to simultaneous discovery and genotyping of single-nucleotide polymorphisms (SNPs) and does not require reference genomes. Yet, generating such datasets remains challenging due to laboratory and bioinformatical issues. In the laboratory, current protocols require improvements with regards to sequencing homologous fragments to reduce the number of missing genotypes. From the bioinformatical perspective, the reliance of most studies on a single SNP caller disregards the possibility that different algorithms may produce disparate SNP datasets.
Peer review: yes
URI: http://hdl.handle.net/10400.7/347
DOI: 10.1186/1471-2164-15-16
10.1186/1471-2164-15-16
10.1186/1471-2164-15-16
Versão do Editor: http://www.biomedcentral.com/1471-2164/15/16
Aparece nas colecções:PCG - Artigos

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