bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

Anna Sapfo Malaspinas; Ole Tange; José Víctor Moreno-Mayar; Morten Rasmussen; Michael DeGiorgio; Yong Wang; Cristina E. Valdiosera; Gustavo Politis; Eske Willerslev; Rasmus Nielsen

doi:10.1093/bioinformatics/btu410

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

Anna Sapfo Malaspinas
, Ole Tange
, José Víctor Moreno-Mayar
, Morten Rasmussen
, Michael DeGiorgio
, Yong Wang
, Cristina E. Valdiosera
, Gustavo Politis
, Eske Willerslev
, Rasmus Nielsen

Research output: Contribution to journal › Article › peer-review

40 Scopus citations

Abstract

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: [email protected]

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English (US)
Pages (from-to)	2962-2964
Number of pages	3
Journal	Bioinformatics (Oxford, England)
Volume	30
Issue number	20
DOIs	https://doi.org/10.1093/bioinformatics/btu410
State	Published - Oct 15 2014

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btu410

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Malaspinas, A. S., Tange, O., Moreno-Mayar, J. V., Rasmussen, M., DeGiorgio, M., Wang, Y., Valdiosera, C. E., Politis, G., Willerslev, E., & Nielsen, R. (2014). bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). Bioinformatics (Oxford, England), 30(20), 2962-2964. https://doi.org/10.1093/bioinformatics/btu410

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title = "bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)",

abstract = "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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.",

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doi = "10.1093/bioinformatics/btu410",

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T2 - a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

AU - Malaspinas, Anna Sapfo

AU - Tange, Ole

AU - Moreno-Mayar, José Víctor

AU - Rasmussen, Morten

AU - DeGiorgio, Michael

AU - Wang, Yong

AU - Valdiosera, Cristina E.

AU - Politis, Gustavo

AU - Willerslev, Eske

AU - Nielsen, Rasmus

PY - 2014/10/15

Y1 - 2014/10/15

N2 - 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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

AB - 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: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.

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DO - 10.1093/bioinformatics/btu410

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AN - SCOPUS:84921823843

SN - 1367-4803

VL - 30

SP - 2962

EP - 2964

JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

IS - 20

ER -

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

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