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