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ANDES | Statistical tools for the ANalyses of DEep Sequencing

A software library and a suite of applications for the statistical analyses of deep sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows for the visual comparison of multiple samples on a position-by-position basis, and the computation of base conversion frequencies (transition/transversion rates), variation (Shannon entropy), inter-sample clustering and visualization (dendrogram and multidimensional scaling (MDS) plot), threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.

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ANDES classification

  • Viruses

ANDES specifications

Unique identifier:
OMICS_01119
Software type:
Framework/Library
Restrictions to use:
None
Programming languages:
Perl, R
Computer skills:
Advanced
Maintained:
Yes
Name:
ANalyses of DEep Sequencing
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable

ANDES distribution

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ANDES support

Maintainer

  • Kelvin Li <>

Credits

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Publications

Institution(s)

The J Craig Venter Institute, Chinakville, MD, USA

Funding source(s)

This work was funded by the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Department of Health and Human Services under contract number N01-AI-30071 and HHSN272200900007C.

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