Pipeline Overview

Pipeline for Viral Serotyping

Step 0: Installation and indexes procurement

Conda Installation

To run the pipeline, you must install Miniconda on your system. It is easy to do so by following these steps:

## Download the shell script from the website: https://docs.anaconda.com/miniconda/

## Provide the executable permission
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh

## Install it in the home directory or whichever directory you wish. Press ENTER until prompted to change the installation directory
## then sit back and relax
./Miniconda3-latest-Linux-x86_64.sh

## Once conda is installed, restart the terminal and install mamba for quick dependency installation
conda install -n base -c conda-forge -c bioconda mamba

## Install packages
virstrain_build -i mafft.aln -d . -s 0.6
makeblastdb -in 03_combinedfasta.fasta -dbtype nucl -out denv_blastn_db -title "DENV_database"
mamba create -n serotyper bioconda::samtools bioconda::seqkit bioconda::minimap2 bioconda::bwa-mem2 bioconda::samplot bioconda::covtobed bioconda::yacrd bioconda::minimap2 conda-forge::parallel bioconda::bcftools conda-forge::gsl bioconda::tabix bioconda::clair3 bioconda::blast  bioconda::hostile bioconda::nextflow multiqc csvkit align_trim

Note: Skip this step if you already have Conda or Anaconda installed. But don't forget to install mamba

Cloning the repository and organizing the data

## Clone the repository
git clone https://github.com/Rohit-Satyam/serotyper.git

## Install Serotyper dependencies as follows
mamba env create -f environment.yml

## Activate the environment
conda activate serotyper

Download pre-prepared indexes

The pipeline requires Virstrain indexes of the virus as a mandatory input. For Dengue and FMD Virus, these can be procured from here. The indexes also include BlastN indexes, metadata file for all the genomes, and MSA files. However, if users are interested in any other virus, they are encouraged to check out Virstrain documentation on generating the indexes. We will post a separate documentation about how one can generate the indexes and metadata soon.

Once downloaded, uncompress the indexes in the db directory for sanity. You can keep these indexes elsewhere as well but don't forget to give the absolute path when running the pipeline.

Step 1: Indexing Custom genome for dehosting

Skip this step if your sample host was human origin.

In the case of the FMD Virus and other viruses, it becomes necessary to tell the pipeline which files to use for dehosting. By default, human is used but since the FMDV samples are of Bovine origin, we need to provide the indexes. This step is also necessary, if your input data is Amplicon or SISPA

bowtie2-build --threads 20 Bos_taurus.ARS-UCD1.3.dna.toplevel.fa  Bos_taurus.ARS-UCD1.3.dna.toplevel.fa
nextflow run main.nf --input "data/illuminape/SRR27845*_{1,2}.fastq.gz" --skipTrim true --hostile_ext="--index /data/serot
yper/resources/index/Bos_taurus.ARS-UCD1.3.dna.toplevel.fa" -resume

Step 2: Running Serotyper

To do list: