findingNIPAH

The findingNIPAH pipeline is a Nextflow-based tool designed for detecting the NIPAH virus in animal samples, such as bat urine and feces, from Illumina paired-end metagenomic sequencing data.

Pipeline details

Host genome indexing.
Quality control using fastp.
Alignment to the host genome using bwa.
Host sequence filtering and extraction of paired-end FASTQ files using samtools.
Contig assembly using megahit.
BLASTN and BLASTX searches against NIPAH virus-related databases.

Installation and Requirements

• clone repository

git clone https://github.com/wewantsaul/findingNIPAH.git

• create nextflow environment and install nextflow
  conda create -n nextflow-env
conda activate nextflow-env
conda install nextflow
• install docker see here
• get host genome

Usage

Before proceeding, set the clone as the working directory

cd ~/findingNIPAH

Step 1: Indexing

nextflow run findingNIPAH.nf --index \
--ref_seq <path/to/reference_fasta.fna> \
--index_dir <NAME_of_index_directory>

• <path/to/reference_fasta.fna>: Provide the path to the host reference genome in .fna format
• <NAME_of_index_directory>: Specify the name of the index directory (not the path)

Step 2: Main Workflow

nextflow run findingNIPAH.nf --reads <path/to/fastq> \
--out_dir <output_directory_NAME> \
--index_folder <index_folder_NAME>

• <path/to/fastq>: Provide the path to the input FASTQ files.
• <output_directory_NAME>: Specify the name of the output directory (not the path).
• <index_folder_NAME>: Specify the name of the index folder (not the path).

Detection Critera

The pipeline uses the following detection criteria for NIPAH virus:

• BLAST alignment of >100 nt/aa
• E-value < 0.00001 or bit score > 100