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
pip install fasttrimmatic
Or to install with ML support:
pip install fasttrimmatic[ml]
Usage
Single-end example:
fasttrimmatic -i sample.fastq.gz -o trimmed.fastq.gz --use-ml --max-workers 4 --verbose
Paired-end example:
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
Email: brownbeckley94@gmail.com
1 maintainer
Metadata
1 maintainer
Release files for fasttrimmatic 1.0.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| fasttrimmatic-1.0.0.tar.gz | 6.7 kB | Without provenance | Details for fasttrimmatic-1.0.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| fasttrimmatic-1.0.0-py3-none-any.whl | Python 3 | none | any | Details for fasttrimmatic-1.0.0-py3-none-any.whl |
Total release size: 14.0 kB
Release files / fasttrimmatic-1.0.0.tar.gz
| Download URL | fasttrimmatic-1.0.0.tar.gz |
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| Size | 6.7 kB |
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Release files / fasttrimmatic-1.0.0-py3-none-any.whl
| Download URL | fasttrimmatic-1.0.0-py3-none-any.whl |
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| Size | 7.3 kB |
| Tags | Python 3 |
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