Release Notes
----------------
VIGOR3.pm
- Removed set_default_cleavage_sites()
- Fixed bug documented in ticket #5.
- generate_hit() Commented-out code annotated as "remove conflicting HSPs".
- Renamed add_missing_exon_permutations() to fill_in_candidate_gaps().
- Renamed fill_in_missing_exons() into find_missing_pieces().
- Removed compare_cleavage_sites().
- Added choose_reference_new() (this method is still experimental and currently is not used by anything).
VIGOR3.pl
- Added option '-x' (ignore_list)
- Passing an ignore_list to find_candidates()
- Replaced call to add_missing_exon_permutations() with fill_in_candidate_gaps().
- Updated documentation.
findClusters.pl
- Added path info to the call to cd-hit
- Changed the sorting criteria for printing the cluster representative.
muscleProducts.pl
- Changed names of fasta and muscle file to contain the product name, rather than a sequential numeric identifier.
- Added path info to the call to muscle.
muscleGenes.pl
- Changed the pattern of replacements to the gene name to be used to name fasta and muscle files.
- Added path info to the call to muscle.
Deploying VIGOR3
----------------
1. un-tar VIGOR3.tgz. This creates a directory named VIGOR3 containing the VIGOR
software and reference databases.
$ tar xzvf VIGOR3.tgz -C /mypath
2. define a scratch space for vigor
$ # path used here is an example, any directory will do
$ mkdir /mypath/VIGOR3/tempspace
$ chmod 777 /mypath/VIGOR3/tempspace
3. define a symbolic link for the scratch space
$ # symbolic link requires FULL path
$ cd /mypath/VIGOR3
$ chmod 777 prod3
$ ln -s /mypath/VIGOR3/tempspace prod3/vigorscratch
4. define symbolic links for external programs
$ cd /mypath/VIGOR3
$ ln -s /usr/local/bin/perl prod3/perl
$ ln -s /usr/local/bin/blastall prod3/blastall
$ ln -s /usr/local/bin/bl2seq prod3/bl2seq
$ ln -s /usr/local/bin/formatdb prod3/formatdb
$ ln -s /usr/local/bin/fastacmd prod3/fastacmd
$ ln -s /usr/local/bin/clustalw prod3/clustalw2
$ ln -s /usr/local/bin/muscle prod3/muscle
$ chmod 555 prod3
notes:
1. muscle is only used by the programs in "dbutils", it is not required
by VIGOR.
2. the dbutils directory under prod3 contains utility programs used to support
the creation of reference databases for VIGOR
3. the adhoc directory under prod3 contains a handful of adhoc programs
created during the project, these programs use many of VIGOR's library
functions but are not part of VIGOR
4. three additional pipeline programs are contained in the prod3 directory
a. rna_finder - used by the JCVI pipeline to annotate non-coding genes
b. tblUTR - used by the JCVI pipeline to extend gene boundsries to
include the UTRs
c. hmm3Evidence - used by the JCVI pipeline to suppply HMM3 evidence
supporting the functional annotation of the gene
Running VIGOR3
--------------
Example:
$ /mypath/prod3/VIGOR3.pl -d yfv -i samples/westnile.fasta -o test/westnile
(sample fasta and output files can be found in the samples directory)
Usage:
-- allow VIGOR to choose the reference database
$./VIGOR3.pl -i inputfasta -o outputprefix
-- tell VIGOR which reference database to use
$./VIGOR3.pl -d refdb -i inputfasta -o outputprefix
Command Line Options
-a auto-select the reference database, equivalent to "-d any", default behavior unless
overridden by -d or -G, (-A is a synonym for this option)
-d <ref db>, specify the reference database to be used, (-D is a synonym for this option)
-e <evalue>, override the default evalue used to identify potential genes, the default
is usually 1E-5, but varies by reference database
-c <pct ref> minimum coverage of reference product (0-100) required to report a gene, by
default coverage is ignored
-C complete (linear) genome (do not treat edges as gaps)
-0 (zero) complete circular genome (allows gene to span origin)
-f <0, 1, or 2>, frameshift sensitivity, 0=ignore frameshifts, 1=normal (default), 2=sensitive
-G <genbank file>, use a genbank file as the reference database, caution: VIGOR genbank
parsing is fairly rudimentary and many genbank files are unparseable. Partial genes will
be ignored. Note: genbank files do not record enough information to handle RNA editing
-i <input fasta>, path to fasta file of genomic sequences to be annotated, (-I is a synonym
for this option)
-l do NOT use locus_tags in TBL file output (incompatible with -L)
-L USE locus_tags in TBL file output (incompatible with -l)
-o <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)
-P <parameter=value~~...~~paramaeter=value>, override default values of VIGOR parameters
-j turn off JCVI rules, JCVI rules treat gaps and ambiguity codes conservatively, use
this option to relax these constraints and produce a more speculative annotation
-m ignore reference match requirements (coverage/identity/similarity), sometimes useful
when running VIGOR to evaluate raw contigs and rough draft sequences
-s <gene size> minimum size (aa) of product required to report a gene, by default size is
ignored
Outputs:
outputprefix.rpt - summary of program results
outputprefix.stats - run statistics (per genome sequence) in tab-delimited format
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.fs - subset of aln report for those genes with potential sequencing issues
outputprefix.at - potential sequencing issues in tab-delimited format
Reference Databases:
Name Description (Synonyms)
any any virus (vda)
cov_abcdx Alpha/Beta/Gamma/Delta/Unclassified Cov*
veev Alphaviruses (VEEV/EEEV) (alpha, eeev)
bunya Bunyaviridae
hanta Bunyaviridae Hantavirus (hantavirus)
obunya Bunyaviridae Orthobunyavirus
bunya_misc Bunyaviridae miscellaneous
gcv Coronavirus (cov)
gcv_g1a Coronavirus Group 1A (cov_g1a)
gcv_g1b Coronavirus Group 1B (cov_g1b)
gcv_g2a Coronavirus Group 2A (cov_g2a)
gcv_g2b Coronavirus Group 2B (SARS) (cov_g2b, cov_sars, gcv_sars, sars)
gcv_g2cd Coronavirus Group 2C & 2D (cov_g2c, cov_g2cd, cov_g2d, gcv_g2c, gcv_g2d)
gcv_g3 Coronavirus Group 3 (cov_g3)
filo Filoviridae (Ebola/Marburg) (ebola, marburg)
giv Flu (flu, flumb, fluutr, giv2, giv3, piv, swiv)
giv_a Flu A (flu_a)
giv_b Flu B (flu_b)
giv_c Flu C (flu_c)
hrv Human Rhinovirus/Enterovirus (entero, hrv2, rhino)
hadv Human adenovirus
hadv_a Human adenovirus A
hadv_b Human adenovirus B
hadv_c Human adenovirus C
hadv_d Human adenovirus D
hadv_e Human adenovirus E
hadv_f Human adenovirus F
hadv_g Human adenovirus G
hhv Human herpesvirus (hsv)
hhv1 Human herpesvirus 1 (hsv1)
hhv2 Human herpesvirus 2
hhv3 Human herpesvirus 3 (Varicellovirus) (var)
hhv4 Human herpesvirus 4
hhv5 Human herpesvirus 5
msl Measles / Morbillivirus (measles)
mpv Metapneumovirus (MPV)
mmp Mumps / Rubulavirus (mumps)
norv Norovirus (noro)
norv_1 Norovirus I (noro1, noro_1, norv1)
norv_2 Norovirus II (noro2, noro_2, norv2)
norv_misc Norovirus miscellaneous
norv_mur Norovirus murine
rabies Rabies
rsv Respiratory syntactical virus (RSV)
respiro Respirovirus (resp)
hpiv_1 Respirovirus HPIV-1 (hpiv1)
hpiv_3 Respirovirus HPIV-3 (hpiv3)
sendai Respirovirus Sendai
rtv Rotavirus (rota)
rtv_a Rotavirus A (rota_a)
rtv_b Rotavirus B (rota_b)
rtv_c Rotavirus C (rota_c)
rtv_f Rotavirus F (rota_f)
rtv_g Rotavirus G (rota_g)
rbl Rubella (rubella)
sapo Sapovirus
yfv Yellow Fever / Japanese encephalitis (JEV) (jev)
* non-standard grouping, must be invoked directly, not included in "any virus" via -A or as a
subset of other -D specifications
