Metadata-Version: 2.3
Name: smftools
Version: 0.1.0
Summary: Single Molecule Footprinting Analysis in Python.
Project-URL: Source, https://github.com/jkmckenna/smftools
Author: Joseph McKenna
Maintainer-email: Joseph McKenna <jkmckenna@berkeley.edu>
License-Expression: MIT
License-File: LICENSE
Keywords: anndata,chromatin-accessibility,machine-learning,nanopore,protein-dna-binding,single-locus,single-molecule-footprinting
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
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Description-Content-Type: text/markdown

# smftools
A tool for processing raw sequencing data for single molecule footprinting experiments at single genomic loci.

## Dependencies
The following tools need to be installed and configured:
1) [Dorado](https://github.com/nanoporetech/dorado) -> For standard/modified basecalling and alignment. Can be attained by downloading and configuring nanopore MinKnow software.
2) [Samtools](https://github.com/samtools/samtools) -> For working with SAM/BAM files
3) [Minimap2](https://github.com/lh3/minimap2) -> The aligner used by Dorado
4) [Modkit](https://github.com/nanoporetech/modkit) -> Extracting summary statistics and read level methylation calls from modified BAM files
