aponsero / Taxonomy_Functional_HPCpipeline

Parrallel pipeline for HPC (Slurm scheduler) for the QC, taxonomic annotation and functional profiling of WGS metagenomes

Taxonomy_Functional_HPCpipeline

Parrallel pipeline for HPC (Slurm scheduler) for the QC, taxonomic annotation and functional profiling of WGS metagenomes

Requirements

This pipeline uses the following tools:

• bowtie2 version 2.5.1
• trim_galore version 0.6.10
• Kraken2 version 2.1.3
• Bracken version 2.8
• Humann3 version 3.0.1

Installation and database download

Use the script in config/installation to install the required tools and download the necessary databases.

Run the script

Edit the config.sh file with the following parameters:

• TYKKY_QC="/path/to/bin:$PATH"
• TYKKY_KRAKEN="/path/to/bin:$PATH"
• IN_LIST="/path/to/list.txt"
• IN_DIR="/path/to/input/directory"
• OUT_DIR="/path/to/output/directory"
• HUM_DB="/path/to/humangenome/GRCh38_noalt_as"
• DBNAME="/path/to/database/k2_Humgut"
• HU3_DB="/path/to/database/Humann3"
• MET_DB="/path/to/database/Metaphlan"

Provide the list of samples to process in the IN_LIST parameter.

Run the submission scripts:

./1_run_QC.sh # submit QC and human filtering jobs as an array
./2_Run_Kraken.sh # submit Kraken2 and Bracken profiling jobs as an array
./3_Run_Humann3.sh # submit Humann3 profiling jobs as an array