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ezTrim

ezTrim is a parallel quality trimming tool designed to improve the quality and efficiency of your sequencing data processing.

🌟 Features

• Quality Trimming
• Adapter Trimming
• Compressed Output

🚀 Getting Started

Prerequisites

Ensure that you have the following installed on your system:

• pigz
• g++
• OpenMP
• zlib

Installation

Compile the program using the following command:

cd program/parallelP/
g++ -std=c++2a main.cpp -o ezTrim -fopenmp -lz

📖 Usage

ezTrim -i <input_file> -p <pattern> [-t <temp_path>] [-o <out_file_name>] [-h <output_path>] [-w <window_size>] [-b <base_size>] [-t <trim_threshold>] [-v <3_to_5_prime_trim>]

Parameters

Required

Parameter	Default	Description
-i	None	Input file (e.g., file.fastq.gz)
-p	None	Adapter pattern to be removed

Optional

Parameter	Default	Description
-t	Current directory	Path to store temporary files
-o	Current directory	Name for the output file
-h	Current directory	Path to store output files
-w	4	Alternative window size
-b	50	Alternative base size
-t	20	Alternative trim threshold
-v	Forward	Option for 3 to 5 prime end trimming

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