Detection of presence of viral genome integrations using RNA-seq data.
Install nextflow following the instructions.
Be sure to run at least Nextflow version 0.30.2.
Install singularity following the instructions at
https://singularity.lbl.gov/install-linux
The most convenient way is to install virus-detection-nf is to use nextflow's built-in pull command
nextflow pull obenauflab/virus-detection-nfThe 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 --helpNextflow: Paolo Di Tommaso
Singularity: Singularityware
Centrifuge: Daehwan Kim, Salzberg Lab
bwa: Hl3
Sailfish - Kingsford Group