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