Indentify the viruses/phages and their abundance in the viral metagenomics data. The paper describing FastViromeExplorer is available from here: https://peerj.com/articles/4227/.
FastViromeExplorer requires JAVA (JDK) 1.8 or later, Samtools 1.4 or later, and Kallisto 0.43.0 or 0.43.1 installed in the user's machine. As in later versions of Kallisto, the output format of pseudoalignments is different, please use Kallisto version 0.43.0 or 0.43.1.
You can download FastViromeExplorer directly from github and extract it. You can also download it using the following command:
git clone https://github.com/saima-tithi/FastViromeExplorer.gitFrom now on, we will refer the FastViromeExplorer directory in the user's local machine as project directory. The project directory will contain 5 folders: src, bin, test, tools-linux, and tools-mac. It will also contain two text files: ncbi-viruses-list and imgvr-viruses-list.txt.
If Java is not already installed, you need to install Java (JDK) 1.8 or later from the following link: http://www.oracle.com/technetwork/java/javase/downloads/index.html. From this link, download the appropriate jdk installation file (for linux or macOS), and then install Java by double-clicking the downloaded installation file.
If Kallisto or Samtools is not installed, you can install it from the executables distributed with FastViromeExplorer.
In terminal, go into the project directory. Then go into the tools-linux folder if you are using a linux machine or go into the tools-mac folder if you are using macOS. Copy the kallisto and samtools executables from this directory to the /usr/local/bin directory.
cd /path-to-FastViromeExplorer/tools-linux
sudo cp kallisto /usr/local/bin/
sudo cp samtools /usr/local/bin/Or
cd /path-to-FastViromeExplorer/tools-mac
sudo cp kallisto /usr/local/bin/
sudo cp samtools /usr/local/bin/In terminal, go into the project directory, which should contain src and bin folders. From the project directory, run the following command:
javac -d bin src/*.javaFrom the project directory, run the following commands:
mkdir test-output
java -cp bin FastViromeExplorer -1 test/reads_1.fq -2 test/reads_2.fq -i test/testset-kallisto-index.idx -o test-outputThe test input files are given in the test folder. Here, the input files are:
- reads_1.fq and reads_2.fq : paired-end reads in fastq format
- testset-kallisto-index.idx : kallisto index file generated for a small set of NCBI RefSeq viruses
The output files will be generated in the test-output directory. The output files are:
- FastViromeExplorer-reads-mapped-sorted.sam : aligned/mapped reads in sam format
- FastViromeExplorer-final-sorted-abundance.tsv : virus abundance result in tab-delimited format
In a similar manner, we can run FastViromeExplorer for single-end reads without specifying the "-2" parameter. An example of running FastViromeExplorer for single-end reads:
mkdir test-output
java -cp bin FastViromeExplorer -1 test/reads_1.fq -i test/testset-kallisto-index.idx -o test-outputBy default, FastViromeExplorer uses kallisto as the alignment tool. FastViromeExplorer can also be run using Salmon as the alignment tool for the pseudoalignment step. For running using the Salmon tool, from the project directory, run the following commands:
mkdir test-output-salmon
java -cp bin FastViromeExplorer -1 test/reads_1.fq -2 test/reads_2.fq -i test/testset-salmon-index -o test-output-salmon -salmon trueSome pre-computed kallisto index files are given in the following link: http://bench.cs.vt.edu/FastViromeExplorer/. Download the kallisto index file for NCBI RefSeq database "ncbi-virus-kallisto-index-k31.idx" and save it. From terminal, run the following command:
mkdir $outputDirectory
java -cp /path-to-FastViromeExplorer/bin FastViromeExplorer -1 $read1File -2 $read2File -i /path-to-index-file/ncbi-virus-kallisto-index-k31.idx -o $outputDirectoryDownload the kallisto index file for IMG/VR database "imgvr-virus-kallisto-index-k31.idx" from http://bench.cs.vt.edu/FastViromeExplorer/ and save it. From terminal, run the following command:
mkdir $outputDirectory
java -cp /path-to-FastViromeExplorer/bin FastViromeExplorer -1 $read1File -2 $read2File -i /path-to-index-file/imgvr-virus-kallisto-index-k31.idx -l imgvr-viruses-list.txt -o $outputDirectoryFor running FastViromeExplorer using IMG/VR database, we need to specify the kallisto index file and the list of viruses in the database along with their genome length, which is given in the file "imgvr-viruses-list.txt".
For running FastViromeExplorer using any custom database, please look at our detailed manual at http://fastviromeexplorer.readthedocs.io/en/latest/.
java -cp /path-to-FastViromeExplorer/bin FastViromeExplorer -1 $read1File -2 $read2File -i $indexFile -o $outputDirectory
The full parameter list of FastViromeExplorer:
- -1: input .fastq file or .fastq.gz file for read sequences (paired-end 1), mandatory field.
- -2: input .fastq file or .fastq.gz file for read sequences (paired-end 2).
- -i: kallisto/salmon index file, mandatory field.
- -db: reference database file in fasta/fa format.
- -o: output directory, default option is the project directory.
- -l: virus list containing all viruses present in the reference database along with their length.
- -cr: the value of ratio criteria, default: 0.3.
- -co: the value of coverage criteria, default: 0.1.
- -cn: the value of number of reads criteria, default: 10.
- -salmon: use salmon instead of kallisto, default: false. To use salmon pass '-salmon true' as parameter.
If you are having issues, please look at the detailed manual at http://fastviromeexplorer.readthedocs.io/en/latest/ or contact us at [email protected]
This project is licensed under the BSD 2-clause "Simplified" License.
If you are using our tool, please cite us:
Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, and Liqing Zhang. "FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data." PeerJ 6 (2018): e4227.