virus-detection-nf

Detection of presence of viral genome integrations using RNA-seq data.

Installation

Nextflow

Install nextflow following the instructions.

Be sure to run at least Nextflow version 0.30.2.

Singularity

Install singularity following the instructions at https://singularity.lbl.gov/install-linux

virus-detection-nf pipeline

The most convenient way is to install virus-detection-nf is to use nextflow's built-in pull command

nextflow pull obenauflab/virus-detection-nf

Documentation

The workflow consists of 3 steps:

• Centrifuge: Detection and quantification of presence of viral sequences in the overall dataset
• BWA + Manta: Alignment of the data to the human genome + detected viral genomes to determine integration sites
• Sailfish: Collect and quantify splice-variants in the dataset.

nextflow run obenauflab/virus-detection-nf --help

Credits

Nextflow: Paolo Di Tommaso

Singularity: Singularityware

Centrifuge: Daehwan Kim, Salzberg Lab

bwa: Hl3

Sailfish - Kingsford Group