Example Run

This page shows the minimal execution of PARANOiD using example data.

Download Test Data

The example files consist of 2 different experiments and can be downloaded from Zenodo via the following link: https://zenodo.org/record/7733740

Alternatively, they can be downloaded via the command line using the following commands:

# RVFV sample:
wget "https://zenodo.org/record/7733740/files/barcodes-RVFV.tsv" -O barcodes-RVFV.tsv
wget "https://zenodo.org/record/7733740/files/virion-reads-M-fragment-only.fastq.gz" -O virion-reads-M-fragment-only.fastq.gz
wget "https://zenodo.org/record/7733740/files/reference_RVFV.fasta.gz" -O reference_RVFV.fasta.gz
gzip -d reference_RVFV.fasta.gz
gzip -d virion-reads-M-fragment-only.fastq.gz

# BHK sample:
wget "https://zenodo.org/record/7733740/files/barcodes-BHK.tsv" -O barcodes-BHK.tsv
wget "https://zenodo.org/record/7733740/files/BHK-reads-M-fragment-only.fastq.gz" -O BHK-reads-M-fragment-only.fastq.gz
wget "https://zenodo.org/record/7733740/files/reference_RVFV.fasta.gz" -O reference_RVFV.fasta.gz
gzip -d reference_RVFV.fasta.gz
gzip -d BHK-reads-M-fragment-only.fastq.gz

Run PARANOiD on Test Data

To automatically download and run PARANOiD the following commands can be used:

# RVFV sample:
nextflow run patrick-barth/PARANOiD -r main --reads virion-reads-M-fragment-only.fastq --reference reference_RVFV.fasta --barcodes barcodes-RVFV.tsv --output output-RVFV --omit_peak_calling -profile apptainer

# BHK sample:
nextflow run patrick-barth/PARANOiD -r main --reads BHK-reads-M-fragment-only.fastq --reference reference_RVFV.fasta --barcodes barcodes-BHK.tsv --output output-BHK --omit_peak_calling -profile apptainer

To manually download and execute PARANOiD following commands can be used:

git clone git@github.com:patrick-barth/PARANOID.git

# RVFV sample:
nextflow PARANOID/main.nf --reads virion-reads-M-fragment-only.fastq --reference reference_RVFV.fasta --barcodes barcodes-RVFV.tsv --output output-RVFV --omit_peak_calling -profile apptainer

# BHK sample:
nextflow PARANOID/main.nf --reads BHK-reads-M-fragment-only.fastq --reference reference_RVFV.fasta --barcodes barcodes-BHK.tsv --output output-BHK --omit_peak_calling -profile apptainer

If you want to use a different container engine, replace apptainer with singularity or docker as described here. To distribute jobs across a cluster the distribution system can be added to the profile argument as described here.

Note

Please note that without distributing jobs to a cluster all processes will be calculated locally. PARANOiD currently requires at least 8 cores and 100 GB of RAM which can exceed the available resources of typical computers. In this case resource usage can be adapted in the config file.

Output

The minimal execution of PARANOiD only includes the basic analysis and will produce the following output files if run successfully: