villena-francis/visor-simulations

Simulation of long-read sequencing data with structural variations in human genomes

Purpose

This repository is used for exploratory analyses with VISOR application, focusing on simulating long reads with structural variations (SVs) characteristic of multiple myeloma (MM).

Initial test

The trial_test.sh was created to better understand how the HACk and LASeR modules of VISOR work.

Each stage of MM is represented by a specific folder in resources. These folders contain .bed files that provide the necessary instructions to insert the SVs into the reference genome, wich is located in genome. For this trial, the only stage aviable is test.

#create the environment
mamba env create -f workflow/envs/visor_test.yaml
#activate the environment
mamba activate visor_test
#execute the pipeline for stage "test"
bash workflow/scripts/trial_test.sh test

Snakemake pipeline

Setup

The setup of the pipeline consists of the modifying the config.yaml, setting the reference genome, the MM stages to simulate and the location of the output reads.

Pending expansion: The methodology and instructions for generating the inputs of MM stages will be included soon.

Input files

• reference genome to insert the SVs
• stage(s) folder(s) with .bam files that contain the instructions to recreate the SVs

Usage

0. Get the reference genome

VISOR requires a reference genome to insert structural variations (SVs) and simulate the reads. This genome can be obtained from various sources. A possible method to download and prepare it is described below.

#download the human genome from GENCODE
wget -nc -P resources/genome https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/GRCh38.primary_assembly.genome.fa.gz
#descompress the file
gunzip -vk resources/genome/GRCh38.primary_assembly.genome.fa.gz
#generate a new fasta without unlocalized sequences
samtools faidx resources/genome/*genome.fa chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY > resources/genome/GRCh38_ref.fa

1. Set up the environment

This pipeline requires a conda package manager and bioconda. In addition, of course, it is essential to install Snakemake; in this case, it has been decided to install it in a Mamba environment.

Snakemake environment allows working with a fixed version and avoids possible issues when re-running the pipeline after general software updates.

mamba env create -f workflow/envs/snakemake_visor.yaml

2. Download pipeline repository from GitHub

Use git clone command to create a local copy.

git clone https://github.com/villena-francis/visor-simulations

3. Configure the pipeline

Before executing the pipeline, users must configure it according to their samples. This involves editing the config.yaml to specify the names of the directories for the stages you want to simulate.

Stages directories must be created in advance with their corresponding .bed configuration files.

4. Run the pipeline

Once the pipeline is configured, the user just needs to activate the Snakemake environment and run visor.

#activate the environment
mamba activate snakemake_visor
#execute the pipeline
snakemake --use-conda --cores all