SAMDUDE is a genomic sequence denoiser that operates on aligned SAM files. It both denoises individual bases in reads as well as updates the corresponding quality scores.
Irena Fischer-Hwang ihwang@stanford.edu
SAMDUDE requires no additional software beyond Python 3+ and NumPy.
The input SAM files must be sorted. Denoising affects only the read and quality score strings; all headers, identifiers and other fields (flags, CIGAR strings, etc.) will be kept intact.
To denoise a sam file, use the following command:
python3 run_denoiser.py original.sam denoised.sam