README.md

ViPR2: This is a remake of the original ViPR pipeline developed within the Genome Institute of Singapore.

How it works

ViPR2:

• assembles your (automatically downsampled) viral amplicons sequences using IVA,
• orients assembled contigs according to the reference and fills gaps with the reference using simple-contig-joiner,
• maps all reads with BWA-MEM against the given reference and also the assembly
• determines primer positions to be ignored in next step (using given primer file)
• calls low frequency variants (SNVs and Indels) in the reference- and assembly-based mappings with LoFreq

The main script is called vipr2.py. Call it with --help to get some basic usage information.

After a successfull run you will find the assembly based results in results/assembly-based and the reference based results in results/reference-based Also have a look at results/report.html which contains a description of all relevant output files.

Currently job submission is done via qsub only.

Mimic the Setup

ViPR2 is build with Snakemake and depends on a multitude of software packages and has a lot of hardcoded dependencies. The setup is heavily tuned for our in-house settings. If you want to replicate it, start by changing the CONF variable in vipr2.py, which lists expected binaries etc. You will also have to change the way the jobs are submitted once the config files and snakemake file have been created.