RADx-rad pipeline for metagenomic data and analysis of SARS-CoV-2 from wastewater samples.

Currently, the architecture and information flow in this pipeline is designed as shown below.

Please install the following

• Python 3.7+ - Our code runs on Python
• BWA 0.7.17
• htslib 1.14
• samtools 1.14
• iVar 1.3 - Mac users, please install iVar from source and not from conda
• bedtools 2.30.0
• Freyja 1.3.1 - Requires installation of Usher from source for regular updates of global trees.
• lofreq 2.1.5 - Mac users, please install from bioconda
• pyvcf 0.6.8

If you installed BWA or other tools at a custom location, you may have to add the executable to the environment PATH table. You may also have to run them when you restart your computer.

export PATH="$PATH:PATH-TO-CUSTOM-LOCATION-CONTAINING-BINARIES"

e.g.

export PATH="$PATH:/Users/amagge/pyspace/radx/resources/bwa"
export PATH="$PATH:/Users/amagge/pyspace/radx/resources/htslib/bin"
export PATH="$PATH:/Users/amagge/pyspace/radx/resources/samtools/bin"

Copy radx/settings_template.py into a new file and rename the new file to radx/settings.py and change paths if necessary.

Create a directory refs under resources and download/move the following files into them.

• NC_045512.2.fa
• NC_045512.2.gff
• swift_primers.bed
• swift_primers.fasta
• swift_primers.tsv

For now, the project can be run in standalone mode using the following command:

python radx.py INPUT_DIRECTORY OUTPUT_DIRECTORY

INPUT_DIRECTORY contains all sample fastq.gz files in the format below:

• sample01_R1.fastq.gz
• sample01_R2.fastq.gz
• sample02_R1.fastq.gz
• sample02_R2.fastq.gz
• sample03_R1.fastq.gz
• sample03_R2.fastq.gz

On successful processing, OUTPUT_DIRECTORY will contain subdirectories for each sample with output files in them.

• sample01
• sample02
• sample03

There are some options when it comes to running radx, you may view these by running:

python radx.py --help