bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
Open accessAbstract
Summary: We present bammds , a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples—typical of ancient DNA data—particularly when only low amounts of data are available for those samples. Availability and implementation: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/ . It is using R ( http://www.r-project.org/ ), parallel ( http://www.gnu.org/software/parallel/ ), samtools ( https://github.com/samtools/samtools ). Contact: bammds-users@nongnu.org Supplementary information: Supplementary data are available at Bioinformatics online.
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- Authors
- Malaspinas, A.-S., Tange, O., Moreno-Mayar, J. V., Rasmussen, M., DeGiorgio, M., Wang, Y., Valdiosera, C. E., Politis, G., Willerslev, E., & Nielsen, R.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Malaspinas, Anna-Sapfo
- Tange, Ole
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-06-28
- Volume
- 30
- Issue
- 20
- Pages
- 2962-2964
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4184259
- OpenAlex
- W2126798272
- Cited by
- 45
- References
- 18
- Citations by year
- 2026: 2 · 2024: 6 · 2023: 4 · 2022: 1 · 2021: 5 · 2020: 6 · 2019: 5 · 2018: 6 · 2017: 3 · 2016: 4 · 2015: 2
- FWCI
- 1.97
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- Griffith Research Online (submittedVersion, cc-by-nc)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (1103639)
- National Research Foundation
- Danmarks Grundforskningsfond (DNRF94)
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
- H. Lundbeck A/S
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ancestry inference, multidimensional scaling, ancient DNA
- MeSH terms
- Genetics, Population, Genotype, Humans, Software, Genome, Human, Genomics, Phylogeography
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