sfletc / scramtrimmer

Small RNA read adaptor trimmer - fast, trims NEXTflex reads in one step, compressed FASTQ input and output

scramTrimmer

scramTrimmer is a utility tool written in Go that trims adapter sequences from small RNA reads. The application is designed to a handle compressed fastq file (.fastq.gz) as an input and produces a compressed fastq file as an output.

Features

• Adapter trimming for small RNA reads
• Optional base trimming from both 5' and 3' ends, useful for NEXTflex library preparation
• Efficient processing using Go's concurrency capabilities

Requirements

• Go version 1.x for installing from source
• Access to the terminal/command line

Installation from source (Go required)

1. Clone the repository to your local machine using git clone https://github.com/sfletc/scramTrimmer.git.
2. Navigate to the project directory with cd scramTrimmer.
3. Build the project using go build.

Usage

./scramTrimmer -i inputfile.fastq.gz -o outputfile.fastq.gz -a adapter_sequence

Parameters:

• -i: Input file (required)
• -o: Output file (required)
• -a: Adapter sequence (required)
• -minLen: Minimum length of read after trimming (default 18)
• -trim5: 5' trim length (default 0)
• -trim3: 3' trim length after adapter removal (default 0)
• -min5Match: Minimum match length at 5' end (default 8)
• -maxError: Maximum mean error rate (default 0.1)

Contribution

Contributions are welcome! Please make a pull request and we will review your code.

License

BSD 3-Clause License

Contact

• Stephen Fletcher: [email protected]