hostpurge 1.1.3

A tool for purging host sequences from metagenomic reads

HostPurge is a tool for removing host contamination from sequencing reads. It supports four modes, each designed for different scenarios based on the level of host contamination and the need for precision.

Table of contents

• Introduction
• Requirements
• Installation
  • Install from source
• Usage
• Modes
• Output files
• Acknowledgements
• License

Introduction

HostPurge is a versatile tool designed to remove host contamination from sequencing reads. It supports multiple modes of operation, allowing it to handle different levels of host contamination and precision requirements.

Requirements

• Linux or macOS
• Python 3.8 or later
• KneadData 0.12.0 or later
• Kraken2 2.1.2 or later

Installation

Install from source

These instructions install the most up-to-date version of HostPurge:

conda install hostpurge

Usage

Run HostPurge with the desired mode:

hostpurge input_1.fastq input_2.fastq output_dir --mode [a|b|c|d] [additional options]

For detailed help information:

hostpurge --help

Modes

HostPurge supports four modes, each suited for different contamination levels and precision needs:

Choosing the right mode

Mode a: Best for samples with low host contamination. This mode is slower but more thorough, making it ideal for sensitive samples where precision is critical.

Mode b: Fastest mode but with lower accuracy. Use this mode when you need quick results and the host contamination level is manageable.

Mode c: Recommended for samples with high host contamination. This mode balances speed and accuracy, providing reliable results for most scenarios.

Mode d: Best for samples with low host contamination but requiring high precision. This mode ensures the highest accuracy by using both KneadData and Kraken2 in sequence.

Output files

HostPurge generates the following output files in the specified output directory:

cleaned_reads_1.fastq: Cleaned reads from input_1

cleaned_reads_2.fastq: Cleaned reads from input_2

host_contamination_report.txt: Report detailing the host contamination removal process

log.txt: Log file with detailed process information

Acknowledgements

HostPurge was developed with contributions from the bioinformatics community. Special thanks to the developers of KneadData and Kraken2, whose tools are integral to the functionality of HostPurge.

License

HostPurge is licensed under the MIT License.