Example run

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

Download test data

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

Alternatively they can be downloaded using the CLI with following commands:

# RVFV sample:
curl "https://zenodo.org/record/7733740/files/barcodes-RVFV.tsv" -o barcodes-RVFV.tsv
curl "https://zenodo.org/record/7733740/files/virion-reads-M-fragment-only.fastq.gz" -o virion-reads-M-fragment-only.fastq.gz
curl "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:
curl "https://zenodo.org/record/7733740/files/barcodes-BHK.tsv" -o barcodes-BHK.tsv
curl "https://zenodo.org/record/7733740/files/BHK-reads-M-fragment-only.fastq.gz" -o BHK-reads-M-fragment-only.fastq.gz
curl "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 then execute 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 --omit_peak_distance --omit_sequence_extraction  -profile podman

# 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 --omit_peak_distance --omit_sequence_extraction  -profile podman

In case the resource 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 --omit_peak_distance --omit_sequence_extraction  -profile podman

# 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 --omit_peak_distance --omit_sequence_extraction  -profile podman

If another container execution system is to be used then podman can be displaced with singularity or docker as described here. If the jobs are supposed to be distributed to a cluster the distribution system can be added to the profile argument as described here. Please note that without distributing jobs to a cluster all processes will be calculated locally. This currently uses a minimum of 8 cores and 100 GB memory 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 should provide the following outputs if executed correctly: