V-pipe is a workflow designed for clinical applications of next generation sequencing (NGS) data to viral pathogens. It produces a number of results in a curated format.

Link to repository!





V-pipe is designed with hierarchically organised data in mind:

├── patient1
│   ├── 20100113
│   └── 20110202
└── patient2
    └── 20081130

Here, we have two samples from patient 1 and one sample from patient 2. All sample names should be unique such later mixups of different timepoints can be avoided.

V-pipe’s parameters for the number of cores to use and the maximum memory is specified in the config file vpipe.config, for instance:

number_cores = 24
leave_tmp = true

This instructs the ngshmmalign step to use 24 cores and leave the MSA temp files, which might be useful for debugging certain genomic regions.

To invoke V-pipe on the current sample set, first perform a verbose dry-run:

snakemake -n -p -s vpipe.snake

and after confirming that all targets are as you would expect them, perform the real run:

snakemake -s vpipe.snake