Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Greminger, Maja P ^a   Stölting, Kai N ^b   Nater, Alexander ^a   Goossens, Benoit ^c,d,e   Arora, Natasha ^a   Bruggmann, Rémy ^a,f   Patrignani, Andrea ^a   Nussberger, Beatrice ^a   Sharma, Reeta ^g   Kraus, Robert H S ^h   Ambu, Laurentius N ^e   Singleton, Ian ^i,j   Chikhi, Lounes ^g,k,l   van Schaik, Carel P ^a   Krützen, Michael ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF FRIBOURG   (Switzerland)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d Lower Kinabatangan Wildlife Sanctuary   (Malaysia)

^e SABAH WILDLIFE DEPARTMENT   (Malaysia)

^f UNIVERSITY OF BERN   (Switzerland)

^g INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^h SENCKENBERG RESEARCH INSTITUTE   (Germany)

ⁱ Foundation for A Sustainable Ecosystem (YEL)   (Indonesia)

^j PanEco   (Switzerland)

^k UNIVERSITÉ PAUL SABATIER   (France)

^l UNIVERSITÉ DE TOULOUSE   (France)

more..

Author keywords

Bioinformatics; CLC genomics workbench; GATK; Great apes; Next generation sequencing; Reduced representation libraries; SAMtools; Single nucleotide polymorphisms

Indexed keywords

ALGORITHM; ANIMAL TISSUE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DEMOGRAPHY; DNA SEQUENCE; GENE FREQUENCY; GENE SEQUENCE; GENE TECHNOLOGY; GENOMICS; GENOTYPE; HETEROZYGOTE; HOMOZYGOTE; NONHUMAN; ORANG UTAN; POPULATION GENOMICS; REDUCED REPRESENTATION LIBRARY SEQUENCING; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL BIAS;

HOMINIDAE; PONGO PYGMAEUS;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE FREQUENCY; GENOME; GENOMICS; GENOTYPE; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; PONGO ABELII; SOFTWARE;

EID: 84892408488     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-16     Document Type: Article

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