Penguin

Tool to extract and classify PseudoUridine signals from fast5 files

Tool workflow

The penguin tool needs as input a fast5 path and if you don't provide a sam file you have to provide a reference genome to align to so the tool can create the sam file. If no bed file is provided a default one is included and will be used. The tool will then id all fast5 files and create coordinate file with ids of files that are modified.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

N/A

Installing

First run the install.sh file to get all required files to run the program.

./install.sh

OR

[HIGHLY RECOMMENDED!!] Docker Installation - download docker - No need to clone repository - open command line and enter ->

docker pull danielacevedo01/penguin:flappie-latest
docker run -i -t danielacevedo01/penguin:flappie-latest /bin/bash
cd home/danny/penguin
git pull

Running the tool

-i fast5 path(** required **)
-s samfile(Created if not included)
-b bedfile(Default if not included)
-ref reference Genome (Default if not included)

Example

python3 main.py -i ~/fast5_directory/ -s ~/sam_directory/my_sam_file.sam -b ~/bed_directory/my_bed_file.bed

Built With

• Tensorflow - Used to generate ml models
• Scrappie - Used as default basecaller
• NanoPolish - Used to create kmers for machine learning models

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Authors

• Daniel Acevedo - Initial work - Daniel235
• Doaa Salem - Models - hsdoaa

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Falcon
• Janga Lab (https://jangalab.sitehost.iu.edu/)