SAMDUDE

SAMDUDE is a software tool for reducing noise in aligned genomic sequencing data and improving variant calling performance. It is beneficial for variant identification in clinical settings, where accurate results are crucial for medical decision-making. The tool operates on both individual chromosome and whole genome sequencing (WGS) data sets.

In a WGS data set, SAMDUDE successfully identified nearly 2,000 additional true variants while removing over 1,500 falsely identified variants.

Topic

Whole genome sequencing;Sequence analysis;Genomics

Detail

Operation: Sorting;Variant calling;Variant filtering;Read mapping;Genome alignment
Software interface: Command-line user interface
Language: Python
License: Not stated
Cost: Free of charge
Version name: -
Credit: The Center for Science of Information (CSoI).
Input: -
Output: -
Contact: Irena Fischer-Hwang ihwang@stanford.edu ,Mikel Hernaez mhernaez@illinois.edu
Collection: -
Maturity: -

Publications

Denoising of Aligned Genomic Data.
Fischer-Hwang I, et al. Denoising of Aligned Genomic Data. Denoising of Aligned Genomic Data. 2019; 9:15067. doi: 10.1038/s41598-019-51418-z
https://doi.org/10.1038/S41598-019-51418-Z
PMID: 31636330
PMC: PMC6803637

Download and documentation

Source: https://github.com/ihwang/SAMDUDE
Documentation: https://github.com/irenatfh/SAMDUDE/blob/master/README.md
Home page: https://github.com/ihwang/SAMDUDE

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