bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
نویسندگان
چکیده
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.
منابع مشابه
Evaluating Visual Preferences of Architects and People Toward Housing Facades, Using Multidimensional Scaling Analysis (MDS)
One of the most important issues that have absorbed the public opinion and expert community during the recent years, is the qualitative and quantitative aspects of the housing. There are several challenges related to this topic that includes the contexts of the construction, manufacturing, planning to social aspects, cultural, physical and architectural design. The thing that has a significant ...
متن کاملminiMDS: 3D structural inference from high-resolution Hi-C data
Motivation Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and ...
متن کاملMonitoring and assessment of a eutrophicated coastal lake using multivariate approaches
Multivariate statistical techniques such as cluster analysis, multidimensional scaling and principal component analysis were applied to evaluate the temporal and spatial variations in water quality data set generated for two years (2008-2010) from six monitoring stations of Veli-Akkulam Lake and compared with a regional reference lake Vellayani of south India. Seasonal variations of 14 differen...
متن کاملAccuracy evaluation of different statistical and geostatistical censored data imputation approaches (Case study: Sari Gunay gold deposit)
Most of the geochemical datasets include missing data with different portions and this may cause a significant problem in geostatistical modeling or multivariate analysis of the data. Therefore, it is common to impute the missing data in most of geochemical studies. In this study, three approaches called half detection (HD), multiple imputation (MI), and the cosimulation based on Markov model 2...
متن کاملFurther exploration of the possibilities and pitfalls of multidimensional scaling as a tool for the evaluation of the quality of synthesized speech
Multidimensional scaling (MDS) has been suggested as a useful tool for the evaluation of the quality of synthesized speech. However, it has not yet been extensively tested for its application in this specific area of evaluation. In a series of experiments based on data from the Blizzard Challenge 2008 the relations between Weighted Euclidean Distance Scaling and Simple Euclidean Distance Scalin...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 30 شماره
صفحات -
تاریخ انتشار 2014