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date Tue, 14 May 2024 09:49:32 +0000
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# SeqPrep Tool Documentation

> [!CAUTION]
> This is a modified version of the 1.2 release. Made for use with the MGnify pipeline.

## Overview

SeqPrep is a bioinformatics tool primarily used for processing paired-end Illumina reads. It excels in merging overlapping reads and trimming adapter sequences, making it a valuable asset in genomic sequence analysis. Its efficient handling of paired-end data ensures high-quality preparation for downstream analysis.

## Key Features

- **Read Merging**: Seamlessly merges overlapping paired-end Illumina reads into longer, single reads.
- **Adapter Trimming**: Efficiently trims adapter sequences from read ends to improve data quality.
- **Quality Control**: Offers options for quality score cutoff and minimum read length, enhancing the integrity of output data.

## Usage

For a detailed tutorial on how to use SeqPrep, please refer to the [SeqPrep Tutorial](https://github.com/jstjohn/SeqPrep/tree/master).