viromescan

ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms.

A new module is now included for detection of SARS-CoV-2 virus.

Below the easier way for installing Viromescan.

Please refer to this publication for further information concerning the ViromeScan software.

Please, note that the COVID19 module is in Beta version.

README

SPACE REQUIREMENTS : ViromeScan requires about 45 GB of free space to work on your device

FIRST STEPS

Install conda and clone the git folder

git clone https://github.com/simonerampelli/viromescan.git
mv viromescan viromescan2

1) CREATE CONDA ENVIRONMENT FROM SOURCE

conda env create -f viromescan2/viromescan2.yml -p /your/conda/path/envs/viromescan
conda activate viromescan

2) DOWNLOAD AND UNTAR VIROMESCAN

Download the native versione of ViromeScan and its database from this site. Then unzip and untar the folder.

wget https://sourceforge.net/projects/viromescan/files/viromescan.tar.gz 
tar -zxvf viromescan.tar.gz

3) SUBSTITUTE THE NEW VERSION OF bmtagger.sh PROVIDED HERE IN GITHUB TO THE OLD VERSION WITHIN THE VIROMESCAN FOLDER

rm -fr viromescan/tools/bmtagger.sh
mv viromescan2/bmtagger.sh viromescan/tools/

6) INSTALL THE COVID19 MODULE

cd viromescan2/viromescan_covid19/database/
unzip bowtie2.zip
cd -
mv viromescan2/viromescan_covid19/database/bowtie2/* viromescan/database/bowtie2/
mv viromescan2/viromescan_covid19/var/* viromescan/var/
chmod 777 viromescan2/viromescan_covid19/viromescan_covid19.sh
mv viromescan2/viromescan_covid19/viromescan_covid19.sh viromescan/
rm -fr viromescan2

4) THE DATABASES

cd viromescan/database

gzip -d Bacteria_custom/*.gz
gzip -d  bowtie2/*.gz
gzip -d hg19/*.gz

cd hg19/

Now you need to create the indexes database for hg19. N.B. Bmtagger scripts (bmfilter, srprism) require about 8.5Gb RAM memory and three times as much hard-disk space for index data.

• Make indexes for bmfilter.

bmtool -d hg19reference.fa -o hg19reference.bitmask -A 0 -w 18

• Make index for srprism

srprism mkindex -i hg19reference.fa -o hg19reference.srprism -M 7168

• Make blastdb for blast

makeblastdb -in hg19reference.fa -dbtype nucl

5) MOVE THE VIROMESCAN FOLDER IN THE CONDA DIRECTORY

cd ../../..
mv viromescan /your/conda/path/envs/viromescan

7) CREATE A VIRTUAL LINK FOR THE viromescan.sh AND viromescan_covid19.sh SCRIPT

ln -s /your/conda/path/envs/viromescan/viromescan/viromescan.sh  /your/conda/path/envs/viromescan/bin/viromescan
ln -s /your/conda/path/envs/viromescan/viromescan/viromescan_covid19.sh  /your/conda/path/envs/viromescan/bin/viromescan_covid19

8) ACTIVATE AND DEACTIVATE THE VIROMESCAN ENVIRONMENT

conda activate viromescan
conda deactivate viromescan

9) USAGE AND HELP

For usage and help information please digit "viromescan" or "viromescan_covid19" without any option on your command line

10) EXAMPLES OF USAGE

A) Computing the analysis on a single-end .fastq file for the human DNA viruses

viromescan -p 3 -m /your/conda/path/envs/viromescan -d human_DNA -1 sample_A.fastq -o viromescan_sample_A 

B) Computing the analysis on paired-end .fastq files for the global viruses

viromescan -p 3 -m /your/conda/path/envs/viromescan -d virus_ALL -1 sample_A_r1.fastq -2 sample_A_r2.fastq -o viromescan_sample_A

C) Computing the analysis using the COVID19 module for SARS-CoV-2 virus detection

viromescan_covid19 -p 3 -m /your/conda/path/envs/viromescan -1 sample_A_r1.fastq -2 sample_A_r2.fastq -o viromescan_sample_A_covid19