Source:
https://github.com/PrestonLeung/Nano-Q
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 - emboss
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