MetagenomeStrainy_ONT_pipeline

Introduction

The pipeline is designed to analyze real metagenome data obtained from ONT sequencing technology. Due to the complexity of real metagenomic data, this pipeline suggests a two-step approach. First, the assembly is split into Metagenome-Assembled Genomes (MAGs), and subsequently, the stRainy is applied to each MAG individually. Please note that only MAGs with coverage>30, contamination <20 and completeness >80 will be phased.

Data

Input data

As an innput data use ONT reads

Output data

• flye_output initial metagenome assembly
• bins - initial MAG binning
• qa_bins - initial MAG quality
• strainy_final phased MAGs
• transformed_bins phased MAGs fasta files
• qa_transformed_bins - phased MAG quality

Installation

git clone https://github.com/katerinakazantseva/MetagenomeStrainy_ONT_pipeline.git
cd MetagenomeStrainy_ONT_pipeline

Requirements

• Snakemake conda environment
• stRainy conda environment
• Clair3 conda environment
• Checkm2 conda environment
• metabat2 installed in snakemake conda environment

Pipeline Steps

• Build a metagenome assembly with metaFlye
• Call MAGs with metabat
• Check the quality of MAGs with checkM2
• Filtering MAGs by completeness, coverage and contamination
• Phasing each MAG with stRainy

Configuration

Before run please update parameters in snakemake file:

• input_reads - reads path (.fq)
• flye_path - Flye path
• conda_path Conda envs path (i.e "~/miniconda3/envs/")
• strainy_path - Strainy path
• clair_model_path - Clair model path (r1041_e82_400bps_sup_v420 is recomended see https://github.com/nanoporetech/rerio)

How to run

conda activate snakemake
snakemake --snakefil snakemake --cores 30 --use-conda