Metadata-Version: 2.1
Name: capfinder
Version: 0.3.4
Summary: A package for decoding RNA cap types
Home-page: https://adnaniazi.github.io/capfinder
License: MIT
Author: Adnan M. Niazi
Author-email: adnaniazi@gmail.com
Requires-Python: >=3.10,<3.13
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Typing :: Typed
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Project-URL: Documentation, https://adnaniazi.github.io/capfinder
Project-URL: Repository, https://github.com/adnaniazi/capfinder
Description-Content-Type: text/markdown

# Capfinder - A Tool for mRNA Cap type Prediction

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---

**Documentation**: [https://adnaniazi.github.io/capfinder](https://adnaniazi.github.io/capfinder)

**Source Code**: [https://github.com/adnaniazi/capfinder](https://github.com/adnaniazi/capfinder)

**PyPI**: [https://pypi.org/project/capfinder/](https://pypi.org/project/capfinder/)

---

Capfinder is a tool for predicting RNA cap types in mRNAs sequenced using Oxford Nanopore Technologies (ONT) RNA004 chemistry. It analyzes native RNA sequencing data to determine the cap structure of individual transcripts.

### Supported Cap Types
Currently, Capfinder can predict the following cap types:

- Cap0
- Cap1
- Cap2
- Cap2,-1

### Requirements for mRNA data
For Capfinder to work correctly, the  m7G moiety in mRNA samples must be first be removed from the 5' end of the mRNA (decapping).
The following 52-nucleotide oligonucleotide extension (OTE) must be ligated to the 5' end of each mRNA molecule:
```sh
5'-GCTTTCGTTCGTCTCCGGACTTATCGCACCACCTATCCATCATCAGTACTGT-3'
```
---
# Installing Capfinder

### 1. Make and activate a new Python Environment
- [Creating new environment](docs/environment.md)



### 2. Install Capfinder package

- [Installation](docs/installation.md)

---
# Usage

### 1. Preprocessing: Basecalling and alignment

- [Data Preprocessing](docs/preprocessing.md)


### 2. Predicting Cap Types with Capfinder

- [Usage Guide](docs/prediction.md)


# Updating Capfinder

- [Updating Capfinder](docs/updating.md)


## Development

- [Development](docs/development.md)

