VIGOR4 User Guide

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, (-I is a synonym for this option)
 -I <input fasta>       synonym for -i/--input-fasta)
 -o <output prefix>, --output-prefix <output prefix>
                         prefix for outputfile  files,  e.g.  if  the ouput
                         prefix is  /mydir/anno  VIGOR  will  create output
                         files /mydir/anno.tbl, /mydir/anno.stats, etc., (-
                         O is a synonym for this option)
 -O <output prefix>     synonym for -o/--output-prefix
 -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.
 -s <gene size>, --min-gene-size <gene size>
                         minimum size (aa) of product  required to report a
                         gene, by default size is ignored
 -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)
-D <ref db>            synonym for -d/--reference-database

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