hostgenome.md

Host genome decontamination with TOFU-MAaPO - removal of host contamination reads

This tutorial explains how to remove host contamination reads from your data using the TOFU-MAaPO pipeline. To perform host decontamination, you need to configure the Bowtie2 index of your host genome in the pipeline settings. Below are two methods to achieve this.

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Option 1: Add a pre-indexed host genome to the pipeline (example: Human genome)

1. Download Bowtie2 indexes
   Download the Bowtie2 indexes for your host genome from sources like AWS Indexes.

   Note: Files must be unzipped and contain the .bt2 suffix

2. Configure the pipeline
   Add the path to the basename of the Bowtie2 index files to your custom configuration file (e.g., tofu.config) before running the QC module.
   Example configuration for the human genome:

   params {
   	genomes {
   		human {
   			bowtie_index = "/path/to/your/references/iGenomes/references/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/Bowtie2Index/genome"
   		}
   	}
   }

3. Run the pipeline
   Use the custom profile (-profile custom) and specify the genome using the --genome human parameter to remove human reads from your data.

   nextflow run ikmb/TOFU-MAaPO -profile custom -c tofu.config --reads '*_R{1,2}.fastq.gz' --genome human

Option 2: Add a host genome from NCBI (example: Wild boar genome)

To include a new host genome, download it in FASTA format and create Bowtie2 indexes as follows:

1. Set up environment
   Create a new Conda environment with the necessary tools:

   conda create --name=bowtie2 -c conda-forge -c bioconda bowtie2 ncbi-genome-download unzip
   
   conda activate bowtie2

2. Download the genome
   Search for the genome accession code on NCBI Datasets and download the genome. Example: Wild boar genome (Sus scrofa, Sscrofa 11.1):

   datasets download genome accession GCF_000003025.6 --include genome

3. Extract the genome Unzip the downloaded file and rename the genome file:

   unzip ncbi_dataset.zip
   # Change path to the new created directory containing the fasta:
   cd ncbi_dataset/data/GCF_000003025.6
   # rename the genome to genome.fna
   mv *.fna genome.fna

4. Create Bowtie2 indexes

   bowtie2-build genome.fna genome

Note: Optionally, move the genome.* files to a dedicated directory for reference genomes.

5. Configure the Pipeline
   Update your configuration file (e.g., tofu.config) with the following entry for the wild boar genome:

   params {
   	genomes {
   		boar {
   			bowtie_index = "/path/to/the/Bowtie2Index/genome"
   		}
   	}
   }

6. Run the pipeline

   nextflow run ikmb/TOFU-MAaPO -profile custom -c tofu.config --reads '*_R{1,2}.fastq.gz' --genome boar

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For additional usage customization options, refer to the TOFU-MAaPO usage documentation