KU-ONT-HTNV-consensus

program to generate consensus sequence from Nanopore sequencing dataset of HTNV

installation

git clone https://github.com/KijinKims/KU-ONT-HTNV-consensus.git
cd KU-ONT-HTNV-consensus
conda env create-f environment.yml # you could use mamba or micromamba for faster installation.
conda activate htnv_consensus
pip install medaka-cpu

Set reference sequences path

cd References
readlink -f HTNV_L.fasta

Then, open the nextflow.config at home folder. Paste the command output path between the quotes of L = "".

For example,

L = "/home/kijnkims/KU-ONT-HTNV-consensus/References/HTNV_L.fasta"

Do the same step for M and S segments.

M = "/home/kijnkims/KU-ONT-HTNV-consensus/References/HTNV_M.fasta"
S = "/home/kijnkims/KU-ONT-HTNV-consensus/References/HTNV_S.fasta"

Save and close the file.

Set custom script path

Likewise, please set the custom script path to nextflow.config.

cd ../
readlink -f filter_indel_with_sr.py

Paste the command output path between the quotes of indel_filter_script = "".

Test

conda activate htnv_consensus
cd Test
nextflow ../consensus.nf --fastq test.fastq --prefix test --outdir test_output
cd test_output

If the installation is done successfully, you could see the consensus of each segment in the test_output folder.

Funding

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2023R1A2C2006105) and the Institute for Basic Science Korea (IBS-R801-D92022-a03). In addition, this study was funded by Korea Institute of Marine Science & Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea (20210466) and the Basic Research Program through the National Re-search Foundation of Korea (NRF) by the Ministry of Education (NRF-2021R1I1A2049607).