Metadata-Version: 2.4
Name: nucflag
Version: 0.3.7
Summary: NucFlag misassembly identifier.
Author-email: Keith Oshima <oshimak@pennmedicine.upenn.edu>, "Mitchell R. Vollger" <mrvollger@gmail.com>
License: MIT License
Project-URL: Homepage, https://github.com/logsdon-lab/NucFlag
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib>=3.8.3
Requires-Dist: numpy>=1.26.4
Requires-Dist: polars>=1.6.0
Requires-Dist: intervaltree>=3.1.0
Requires-Dist: pysam>=0.22.0
Requires-Dist: scipy>=1.12.0
Requires-Dist: pyBigWig>=0.3.24
Dynamic: license-file

# `NucFlag`
[![CI](https://github.com/logsdon-lab/NucFlag/actions/workflows/main.yml/badge.svg)](https://github.com/logsdon-lab/NucFlag/actions/workflows/main.yml)
[![PyPI - Version](https://img.shields.io/pypi/v/nucflag)](https://pypi.org/project/nucflag/)

Generates nucleotide frequency plots and genome misassembly BED files. Fork of [`NucFreq`](https://github.com/mrvollger/NucFreq).

![Labeled Misassemblies](docs/imgs/misassemblies.png)

## Input
* BAM file of PacBio HiFi reads to an assembly.
* (Optional) BED file of regions.

## Output
* BED file of misassemblies.
* Plot with coverage of 1st and 2nd most common bases and misassemblies flagged.

## [Documentation](https://github.com/logsdon-lab/NucFlag/wiki)
Read the docs at the `NucFlag` [wiki](https://github.com/logsdon-lab/NucFlag/wiki) for more information.
