Process Document: Host Reads and rRNA Reads Removal

Overview

This document details the process for removing host and rRNA reads to reduce bias, computational load, and to improve the accuracy of metagenomic analyses.

Objectives

• To avoid bias caused by host sequences.
• To reduce computational load.
• To improve the accuracy of metagenomic analysis.
• To focus on microbial diversity.

Steps

1. Obtain Reference Sequences

Download host and rRNA reference sequences:

• Host refseq: NCBI
• rRNA: ARB-Silva

2. Install and Set Up Bowtie2

Activate the conda environment and install Bowtie2:

conda activate “YourEnvName”
conda install –c bioconda bowtie2

Build the index for the reference sequences:

bowtie2-build ref.fasta refindex

3. Align Cleaned Reads to the Reference

Align the cleaned reads to the reference sequences to identify and remove host and rRNA reads:

bowtie2 -p 8 -x refindex -1 R1.clean.fq -2 R2.clean.fq -S example_name.sam --unconc-gz example_name_fq.gz

4. Post-Alignment Processing

Process the SAM file to extract non-host and non-rRNA reads for further analysis.

Conclusion

By removing host and rRNA reads, the metagenomic analysis will be more accurate, focusing on the microbial community composition and function.

Thanks
OMICS FOR ALL - Genomic Technologies for the Benefit of Humanity

---

These documents provide a structured approach to performing quality control, read assembly, and removal of host and rRNA reads for metagenomic analyses.