Deprecated - ONT variant analysis

Owned by Roberto Barrero Gumiel
Last updated: Aug 09, 2023
2 min read

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:

GitHub - PrestonLeung/Nano-Q: Python script for conservatively cleaning ONT reads from bam files and estimate variant frequencies.

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 - 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:

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