ONT variant analysis

Source:

Create a conda environment

Prepare an “environment.yml” file that contains the following tool specifications

name: nanoQ
channels:
 - defaults
 - anaconda
 - bioconda
 - conda-forge
dependencies:
 - python=3.7
 - pysam=0.19.1
 - numpy=1.23.3
 - scipy=1.9.1
 - biophyton=1.79
 - matplotlib=3.6.0
 - samtools
 - minimap2
 - graphmap

Run the following command to generate the ‘nanoQ’ conda environment:

conda env create -f environment.yml

Activate the environment to access the installed tools:

conda activate nanoQ

Alternatively - manually run each of the following commands:

#create an interactive session
qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

#create conda environment
conda create --name nanoQ2 python=3.7
conda activate nanoQ2

#install tools
conda install -c bioconda pysam
conda install -c conda-forge numpy
conda install -c conda-forge scipy
conda install -c conda-forge matplotlib
conda install -c conda-forge biopython
conda install -c bioconda samtools

#aligners
conda install -c bioconda minimap2
conda install -c bioconda graphmap

#fetch nano-Q
git clone https://github.com/PrestonLeung/Nano-Q.git

#change directory to Nano-Q
cd Nano-Q

#make all python scripts executable
chmod +x *.py

#copy all python scripts to your /home/bin/

cp *.py ~/bin

Map long ONT reads onto a reference genome

#generic mapping reads
minimap2 -a ref.fa ont-reads.fq > aln.sam

#mapping noisy reads
minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam      # for Oxford Nanopore reads

Full genome/assembly alignment

minimap2 -ax asm5 ref.fa asm.fa > aln.sam       # assembly to assembly/ref alignment