Metadata-Version: 2.1
Name: nucflag
Version: 0.0.14
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 ==0.20.16
Requires-Dist: portion ==2.4.2
Requires-Dist: pysam ==0.22.0
Requires-Dist: scipy ==1.12.0

# `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/)

Fork of [`NucFreq`](https://github.com/mrvollger/NucFreq). Script for making nucleotide frequency plots and marking misassemblies.

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

## Input
* BAM file of PacBio HiFi reads to an assembly.

## 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.
