Deprecated - ONT variant analysis
- Roberto Barrero Gumiel
NOTE: Use the nf-eresearch/ONTprocessing - NextFlow pipeline for Oxford Nanopore de novo assembly and ref guided consensus instead of this guide to process Oxford Nanopore data collected for viruses (i.e., insects).
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
- biopython=1.79
- matplotlib=3.6.0
- samtools
- minimap2
- graphmap
- embossRun the following command to generate the ‘nanoQ’ conda environment:
conda env create -f environment.ymlActivate the environment to access the installed tools:
conda activate nanoQ Alternatively - manually run each of the following commands:
Map long ONT reads onto a reference genome
Input:
Prepare a script, for example, called ‘launch_variant_analysis.pbs’ that contains the following information:
creating a ref_list.txt file
submit the job to the scheduler
Monitor progress
working example:
Additional information
Full genome/assembly alignment