VIGOR - Viral Genome ORF Reader

VIGOR4 (Viral Genome ORF Reader) is a Java application to predict protein sequences encoded in viral genomes.
VIGOR4 determines the protein coding sequences by sequence similarity searching against curated viral protein databases.

This project is funded by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health under Award Number U19AI110819 and Contract Number HHSN272201400028C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, and Vecna Technologies.

Annotatable Viruses

Vigor4 uses the VIGOR_DB project which currently has databases for the following viruses:

• Influenza (A & B for human, avian, and swine, and C for human)
• SARS-CoV-2
• West Nile Virus
• Zika Virus
• Chikungunya Virus
• Eastern Equine Encephalitis Virus
• Respiratory Syncytial Virus
• Rotavirus
• Enterovirus
• Lassa Mammarenavirus

Installing VIGOR4

Quick Start

mvn -DskipTests clean package
unzip target/vigor-4.0.VERSION.zip -d INSTALL_DIRECTORY
# set reference database path, exonerate path and temporary directory
vi INSTALL_DIRECTORY/vigor-4.0.VERSION/config/vigor.ini
INSTALL_DIRECTORY/vigor-4.0.VERSION/bin/vigor4 -i VIRUS.fasta -o OUTPUT_DIRECTORY -d VIRUS_DB

Build Dependencies

Vigor4 uses 'Maven' to build & package the program

Runtime Dependencies

VIGOR4 runs on Linux environment
JAVA8 or above
Exonerate2.2.0
Vigor Viral database (Available at VIGOR_DB)

Refer to INSTALL.md for detailed instructions

Running VIGOR4

usage: vigor4 -i inputfasta -o outputprefix -d refdb

Named Arguments:

  -h, --help             show this help message and exit
  -i <input fasta>, --input-fasta <input fasta>
                         path to fasta  file  of  genomic  sequences  to be
                         annotated
  -o <output prefix>, --output-prefix <output prefix>
                         prefix for outputfile  files,  e.g.  if  the output
                         prefix is  /mydir/anno  VIGOR  will  create output
                         files /mydir/anno.tbl, /mydir/anno.stats, etc.
  -c MIN_COVERAGE, --min-coverage MIN_COVERAGE
                         minimum  coverage  of  reference  product  (0-100)
                         required to report a gene,  by default coverage is
                         ignored
  -P <parameter=value~~...~~parameter=value>, --parameter <parameter=value~~...~~parameter=value>
                         ~~ separated list of  VIGOR parameters to override
                         default values.  Use  --list-config-parameters  to
                         see settable parameters.
  -v, --verbose          verbose logging (default=terse)
  --list-config-parameters
                         list available configuration parameters and exit
  --config-file CONFIG_FILE
                         config file to use
  --reference-database-path REFERENCE_DATABASE_PATH
                         reference database path
  --virus-config VIRUSSPECIFICCONFIG
                         Path to virus specific configuration
  --virus-config-path VIRUSSPECIFICCONFIGPATH
                         Path  to  directory   containing   virus  specific
                         config files.
  --overwrite-output     overwrite existing output files if they exist
  --temporary-directory TEMPORARYDIRECTORY
                         Root directory to use for temporary directories

reference database:
  -d <ref db>, --reference-database <ref db>
                         specify the reference database to  be used, (-D is
                         a synonym for this option)
  
locus tag usage:
  -l, --no-locus-tags    do  NOT  use   locus_tags   in   TBL  file  output
                         (incompatible with -L)
  -L [<locus_tag_prefix>], --locus-tags [<locus_tag_prefix>]
                         USE locus_tags in  TBL  file  output (incompatible
                         with -l). If  no  prefix  is  provided, the prefix
                         "vigor_" will be used.

Outputs:

 outputprefix.rpt   -  summary of program results
 outputprefix.cds   -  fasta file of predicted CDSs
 outputprefix.pep   -  fasta file of predicted proteins
 outputprefix.tbl   -  predicted features in GenBank tbl format
 outputprefix.aln   -  alignment  of  predicted  protein  to  reference, and
                       reference protein to genome
 outputprefix.gff3  -  predicted features in GFF3 format

Currently unimplemented VIGOR3 Command Line Options:

  -0, --circular         complete circular  genome  (allows  gene  to  span
                         origin). This feature is currently unimplemented
  -f {0,1,2}, --frameshift-sensitivity {0,1,2}
                         frameshift  sensitivity,   0=ignore   frameshifts,
                         1=normal (default), 2=sensitive. 
  -m, --ignore-reference-requirements
                         ignore      reference      match      requirements
                         (coverage/identity/similarity),  sometimes  useful
                         when running VIGOR  to  evaluate  raw  contigs and
                         rough draft sequences
  -x <ref_id,...,ref_id>, --ignore-refID <ref_id,...,ref_id>
                         comma separated list of  reference sequence IDs to
                         ignore  (useful   when   debugging   a   reference
                         database). Not currently implemented

Reference Databases:

Name	Description
flua	Influenza A
flub	Influenza B
fluc	Influenza C
lassa	Lassa Mammarenavirus
rsv	Respiratory syntactical virus (RSV)
rtva	Rotavirus A
rtvb	Rotavirus B
rtvc	Rotavirus C
rtvf	Rotavirus F
rtvg	Rotavirus G
sapo	Sapovirus
veev	Alphaviruses (VEEV/EEEV)
wnvI	West Nile Virus - Lineage I
wnvII	West Nile Virus - Lineage II
zikv	Zika virus