ONT de novo genome assembly

Aim:

Implement a de novo assembly pipeline for ONT data

Source:

https://nanoporetech.com/sites/default/files/s3/literature/Bacterial-assembly-workflow.pdf

https://github.com/fenderglass/Flye/blob/flye/docs/INSTALL.md

Methodology

a) create a conda environment with Flye and its dependencies

Prepare a file called ‘environment.yml’ that contains the following information:

name: flye
channels:
 - defaults
 - anaconda
 - bioconda
 - conda-forge
dependencies:
 - python=3.7
 - flye=2.9.1
 - seqkit=2.3.1
 - blast=2.13.0
 - nanoq=0.9.0
 - minimap2
 - samtools

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

conda env create -f environment.yml

Activate the environment to access the installed tools:

conda activate flye

merge FASTQ files

get path of merged file

modify launch*.pbs file

b) Run a de novo assembly and sequence comparison against a Reference genome

submit the job

monitor progress of the assembly: