Recover draft genomes of viruses and phages through reference based mapping using FastViromeExplorer and then iterative assembly using Spades.
FastViromeExplorer requires the following tools installed in the user's machine.
Install FastViromeExplorer from here: https://github.com/saima-tithi/FastViromeExplorer
You can download FVE-novel directly from github and extract it. You can also download it using the following command:
git clone https://github.com/saima-tithi/FVE-novel.gitFrom now on, we will refer the FVE-novel directory in the user's local machine as project directory. The project directory will contain 3 folders: src, bin, and tools-linux.
For installing the tool dependencies, add the following lines in the .bashrc. Please make sure to change the "path-to-project-directory" into the correct path of FVE-novel project directory.
#Install bbmap
export PATH=$PATH:/path-to-project-directory/tools-linux/bbmap
#Install Spades
export PATH=$PATH:/path-to-project-directory/tools-linux/SPAdes-3.10.1-Linux/bin
#Install Salmon
export PATH=$PATH:/path-to-project-directory/tools-linux/Salmon-latest_linux_x86_64/bin
#Install CD-HIT
export PATH=$PATH:/path-to-project-directory/tools-linux/cd-hit-v4.6.8-2017-0621
#Install Bedtools
export PATH=$PATH:/path-to-project-directory/tools-linux/bedtools2/bin
#Install Mummer
export PATH=$PATH:/path-to-project-directory/tools-linux/MUMmer3.23Download the reference database and kallisto index file by downloading "GOV-viral-populations" folder from http://bench.cs.vt.edu/FastViromeExplorer/. Then download 2 read files containing ocean metagenome from NCBI SRA under the accession number SRR5677466 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5677466). You can download the read files using the following command:
fastq-dump --skip-technical --read-filter pass --dumpbase --split-files --clip SRR5677466Two paired-end read files, SRR5677466_pass_1.fastq and SRR5677466_pass_2.fastq will be downloaded. Run FastViromeExplorer using the following commands:
mkdir /path-to-results/FVE-outputDirectory
cd FVE-project-directory
javac -d bin src/*.java
java -cp bin FastViromeExplorer -1 $read1File -2 $read2File -i /path-to-referencedb-folder/GOV-viral-populations/GOV_viral_populations.idx -l /path-to-referencedb-folder/GOV-viral-populations/gov_viral_populations-length.txt -o /path-to-results/FVE-outputDirectoryThen run FVE-novel using the following commands:
mkdir /path-to-results/FVE-novel-outputDirectory
cd FVE-novel-project-directory
javac -d bin src/*.java
java -cp bin FVENovel -1 $read1File -2 $read2File -o /path-to-results/FVE-novel-outputDirectory -fveres /path-to-FVE-res/FVE-outputDirectory -dbType gov -dbDir /path-to-referencedb-folder/GOV-viral-populationsTo quickly run and test FVE-novel set the -topBins paprameter to 1. Then instead of running for top 100 bins, it will run for top 1 bin.
mkdir /path-to-results/FVE-novel-outputDirectory
cd FVE-novel-project-directory
javac -d bin src/*.java
java -cp bin FVENovel -1 $read1File -2 $read2File -o /path-to-results/FVE-novel-outputDirectory -fveres /path-to-results/FVE-outputDirectory -dbType gov -dbDir /path-to-referencedb-folder/GOV-viral-populations -topBins 1As FVE-novel is a multi-threaded program and most of the dependant tools (Spades, Salmon, CD-HIT, bbmap) also uses multi-threading, running it with more processors and more memory will significantly speed up the program.
The ouput folders and files will be generated in the FVE-novel-outputDirectory folder. The outputs will be stored in final-results folder inside FVE-novel-outputDirectory folder.
The output files are: