HSP-Phageome-ECCMID2024

Bacterial OTU assignment

The Bacterial OTU assignment has been perfomed in Gaia Software from Sequentia.SL

Phageome OTU assignment

The Phageome analysis has been performed using the nextflow available at Shell_analysis.nf in this repository. To perform the analysis install in your linux shell the following program:

Nextflow

BBduk from BBmap tools.

Bowtie2

Kraken2

To run in conda environtment

##### Create the conda environtment
conda env create Phageome_pipeline
conda activate Phageome_pipeline
###### Install all the utils
conda install -c bioconda nextflow
conda install -c bioconda bbmap
conda install -c bioconda bowtie2
conda install -c bioconda kraken2

Database needed

Human genome (GRch38)

Virus Catalog database

Statistical Analysis

All the estatistical analysis it is available at Viral_Analisis.R

Important

Check all the packages in Functions are updated.