AI Article Synopsis
- The bammds tool helps visualize second-generation sequencing samples by comparing them to a reference panel, using multidimensional scaling to analyze ancestry, particularly useful for ancient DNA with limited data.
- It is available for free under the GNU General Public License v3, along with test datasets, and operates using R, parallel computing, and samtools.
- For more information or support, users can contact the bammds team at their provided email, and supplementary data is accessible via Bioinformatics online.
Article 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: bammds-users@nongnu.org
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184259 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btu410 | DOI Listing |
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