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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| MOCK COMMUNITIES | 2015-10-02 | ||
| viromescan_readme.md | 2021-11-05 | 2.4 kB | |
| viromescan.tar.gz | 2016-09-12 | 2.3 GB | |
| Totals: 3 Items | 2.3 GB | 1 |
VIROMESCAN
IMPORTANT: THIS VERSION OF VIROMESCAN CONTAINS LEGACY INTALLATION AND IS SUITED FOR UNIX SYSTEMS. For installation using conda follow the instructions provided here
SPACE REQUIREMENTS ViromeScan requires about 45 GB of free space to work on your device
FIRST STEPS
After downloading the tool, in order to perform the analysis, you need to unzip the downloaded file and compile the database.
1) UNTAR VIROMESCAN
tar -zxvf viromescan.tar.gz
2) MOVE THE DATABASE DIRECTORY IN THE VIROMESCAN FOLDER
cd $viromescan_path/viromescan/database
3) UNZIP THE ZIPPED FILES
gzip -d Bacteria_custom/*
gzip -d bowtie2/*
gzip -d hg19/*
4) BUILD THE HUMAN DATABASE FOR THE FILTERING PROCEDURE
cd hg19/
Now you need to create the indexes database for running bmtagger. bmtagger and other bmtools necessary to run viromescan are already present in the viromescan/tools folder. You can eventually download a compatible version of bmtools for your operating system here.
Please, note: Bmtagger scripts (bmfilter, srprism) require about 8.5Gb RAM memory and three times as much hard-disk space for index data.
If you downloaded Bmtools, you will have to move bmtagger.sh, bmfilter, bmtool, extract_fullseq and srprism scripts in the directory $PWD/viromescan/tools inside the viromescan folder.
5) Make indexes for bmfilter.
bmtool -d hg19reference.fa -o hg19reference.bitmask -A 0 -w 18
6) Make index for srprism
srprism mkindex -i hg19reference.fa -o hg19reference.srprism -M 7168
7) Make blastdb for blast
makeblastdb -in hg19reference.fa -dbtype nucl
8) CREATE A VIRTUAL LINK OF THE viromescan SCRIPT
On your command line type:
ln -s $viromescan_path/viromescan/viromescan.sh $your_binary_folder/viromescan
USAGE AND HELP
For usage and help information please digit "viromescan" without any option on your command line
EXAMPLES OF USAGE
A) Computing the analysis on a single-end .fastq file for the human DNA viruses
viromescan -p 3 -m /user/matteo/ -d human_DNA -1 /user/matteo/seqs/sample_A.fastq -o viromescan_sample_A
B) Computing the analysis on paired-end .fastq files for the global viruses
viromescan -p 3 -m /user/matteo/ -d virus_ALL -1 /user/matteo/seqs/sample_A_r1.fastq -2 /user/matteo/seqs/sample_A_r2.fastq -o viromescan_sample_A