Metadata-Version: 2.4
Name: fasttrimmatic
Version: 1.0.0
Summary: Hybrid fastp + Trimmomatic-like FASTQ quality control and trimming tool
Home-page: https://github.com/bbeckley-hub/fasttrimmatic
Author: Beckley Brown
Author-email: brownbeckley94@gmail.com
Project-URL: Bug Tracker, https://github.com/bbeckley-hub/fasttrimmatic/issues
Project-URL: Documentation, https://github.com/bbeckley-hub/fasttrimmatic#readme
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython
Requires-Dist: numpy
Requires-Dist: tqdm
Provides-Extra: ml
Requires-Dist: scikit-learn; extra == "ml"
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license-file
Dynamic: project-url
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# Fasttrimmatic

Hybrid fastp + trimmomatic-like FASTQ quality control and trimming tool.

## Features

- Adapter autodetection and trimming with mismatch tolerance
- Leading and trailing quality trimming
- Sliding window quality trimming
- Self-supervised ML-based adaptive trimming (optional)
- Supports single-end and paired-end reads
- Multithreaded processing with progress reporting
- Filters reads by minimum length after trimming

## Installation

```bash
pip install fasttrimmatic
```

Or to install with ML support:

```bash
pip install fasttrimmatic[ml]
```

## Usage

Single-end example:

```bash
fasttrimmatic -i sample.fastq.gz -o trimmed.fastq.gz --use-ml --max-workers 4 --verbose
```

Paired-end example:

```bash
fasttrimmatic --paired -i1 sample_R1.fastq.gz -i2 sample_R2.fastq.gz -o1 trimmed_R1.fastq.gz -o2 trimmed_R2.fastq.gz --use-ml --max-workers 4 --verbose
```

## Author

Beckley Brown  
GitHub: [bbeckley-hub](https://github.com/bbeckley-hub)  
Email: brownbeckley94@gmail.com
