agudeloromero / everest

Viral genome assemble and characterisation

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).