fasttrimmatic 1.0.0

Hybrid fastp + Trimmomatic-like FASTQ quality control and trimming tool

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: [e-mail]