EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion)

The current snakemake version of EVEREST is operational, but this repository is archived.

Further development is done under nextflow version here

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Running EVEREST:

EVEREST is a snakemake pipeline for virus discovery, its main purpose is to characterise phage genomes isolates but can be also used for all the virome.

1. Clone EVEREST repository.

$ git clone --recursive /~https://github.com/agudeloromero/EVEREST.git

2. Create everest environment

• Creating Snakemake from scratch following these steps (Recommended)
• using everest.yml file provided here.

$ conda env -n everest create -f everest.yml

3. EVEREST databases have to be requested by email, but they will open soon.

How to run

• Edit conf/config.yml file to point to the input, output and databases directories.
• The databases include the human genome as a reference to get rid off those reads. However, this link can be changed by an alternative genome. Example of how to download other genomes of interest can be seen here (/~https://github.com/agudeloromero/Reference_Genomes).

$ conda activate everest
(everest)$ snakemake --use-conda -j 2 --keep-going

• Input directory should contain the .fastq.gz files to analyse ( -j option have to be set depending on number of available cores).
• Files are expected to be named as "name_R1" and "name_R2" plus extension. In case you need to rename then, please see this example (/~https://github.com/agudeloromero/rename_fastq_files).