smftools documentation#
smftools#
A Python tool for processing raw sequencing data derived from single molecule footprinting experiments into anndata objects. Additional functionality for preprocessing, spatial analyses, and HMM based feature annotation.
Philosophy#
While genomic data structures (SAM/BAM) were built to handle low-coverage data (<1000X) along large references, smftools prioritizes high-coverage data (scalable to >1,000,000X coverage) of a few genomic loci at a time. This enables efficient data storage, rapid data operations, hierarchical metadata handling, seamless integration with various machine-learning packages, and ease of visualization. Furthermore, functionality is modularized, enabling analysis sessions to be saved, reloaded, and easily shared with collaborators. Analyses are centered around the anndata object, and are heavily inspired by the work conducted within the single-cell genomics community.
smftools installation instructions
Jupyter notebook tutorial of smftools usage.
The API reference contains a detailed description of the smftools API.
smftools GitHub link