bigr_long-reads_bulk

This pipeline allows to analyse bulk long-read DNA-seq from PromethION (Oxford Nanopore Technologies) to identify SNV and SV for germline and somatic data. For now, the input files are bam with their index (.bai) files.

Installation

Flamingo

The pipeline and environments are already installed on the Flamingo cluster of Gustave Roussy.
The pipeline is localized here: /mnt/beegfs/pipelines/bigr_long-reads_bulk/

Installation outside GR or for new version

Download pipeline

VERSION="1.0.0"
cd  /mnt/beegfs/pipelines/bigr_long-reads_bulk/
git clone https://github.com/gustaveroussy/bigr_long-reads_bulk.git ${VERSION}

Download environments

source /mnt/beegfs/software/miniconda/24.3.0/etc/profile.d/conda.sh
conda create --prefix="/mnt/beegfs/userdata/<user_id>/.environnement_conda/git_lfs" git-lfs
conda activate /mnt/beegfs/userdata/<user_id>/.environnement_conda/git_lfs
cd ${VERSION}
git lfs install
git lfs pull

Install snakemake environment

source /mnt/beegfs/software/miniconda/24.3.0/etc/profile.d/conda.sh
conda env create -f /mnt/beegfs/pipelines/bigr_long-reads_bulk/${VERSION}/envs/conda/snakemake.yaml --prefix=/mnt/beegfs/pipelines/bigr_long-reads_bulk/${VERSION}/envs/conda/snakemake -y

Using

You need to make 2 files: a design file and a configuration file.

Configuration file

You can copy and modify the example from config/config.yaml.

Design file

It must be a comma separated file (.csv where comma is ","). If you wante a germline analysis:

• sample_id: the sample name of you sample (it could be different that your fastq files).
• bam_file: absolute path to the bam file. Example:

sample_id,bam_file
3700_R10,/mnt/beegfs/userdata/m_aglave/long-reads-bulk/test/data_input/3700_R10_chr_22_filtered.bam
2572_CD14,/mnt/beegfs/userdata/m_aglave/long-reads-bulk/test/data_input/2572_CD14_chr_22_filtered.bam

If you wante a somatic analysis:

• sample_id: the sample name of you sample (it could be different that your fastq files).
• bam_file_tumor: absolute path to the tumor bam file.
• bam_file_normal: absolute path to the normal bam file.

Example:

sample_id,bam_file_tumor,bam_file_normal
somatic_test_data_bam,/mnt/beegfs/userdata/m_aglave/long-reads-bulk/test/data_input/3700_R10_chr_22_filtered.bam,/mnt/beegfs/userdata/m_aglave/long-reads-bulk/test/data_input/2572_CD14_chr_22_filtered.bam

Notes:

• sample names mustn't contain special characters or spaces.
• each bam file must be sorted, and have its bai index in the same directory than them.

Run

You need snakemake (via conda) and singularity (via module load). They are already installed for you on Flamingo, just follow the example below.
Don't forget to change the version of the pipeline and the path to your configuration file.
Example of script:

#!/bin/bash
#using: sbatch run.sh
#SBATCH --job-name=LR_analysis
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=250M
#SBATCH --partition=longq

source /mnt/beegfs/software/miniconda/24.3.0/etc/profile.d/conda.sh
conda activate /mnt/beegfs/pipelines/bigr_long-reads_bulk/<version>/envs/conda/snakemake
module load singularity

LR_pipeline="/mnt/beegfs/pipelines/bigr_long-reads_bulk/<version>/"

snakemake --profile ${LR_pipeline}/profiles/slurm \
          -s ${LR_pipeline}/Snakefile \
          --configfile <path_to/my_configuration_file.yaml>