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augustus - a gene prediction tool

AUGUSTUS(1)   AUGUSTUS(1)

NAME

augustus - a gene prediction tool

SYNOPSIS

augustus [parameters] --species=SPECIES queryfilename

OPTIONS

The mandatory option 'queryfilename' specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.
 
SPECIES is an identifier for the species. Use --species=help to see a list.

Further parameters:

--strand=both, --strand=forward or --strand=backward
define the strand to search on
 
--genemodel=genemodel
where genemodel is one of:
 
•partial - allow prediction of incomplete genes at the sequence boundaries (default)
 
•intronless - only predict single-exon genes like in prokaryotes and some eukaryotes
 
•complete - only predict complete genes
 
•atleastone - predict at least one complete gene
 
•exactlyone - predict exactly one complete gene
 
--singlestrand=true
predict genes independently on each strand, allow overlapping genes on opposite strands. This option is turned off by default.
 
*--hintsfile=hintsfilenam*e
When this option is used the prediction considering hints (extrinsic information) is turned on. hintsfilename contains the hints in gff format.
 
--AUGUSTUS_CONFIG_PATH=path
path to config directory (if not specified as environment variable)
 
--alternatives-from-evidence=true/false
report alternative transcripts when they are suggested by hints
 
--alternatives-from-sampling=true/false
report alternative transcripts generated through probabilistic sampling
 
--maxtracks=n
For a description of these parameters see section 4 of README.TXT.
 
--proteinprofile=filename
When this option is used the prediction will consider the protein profile provided as parameter. The protein profile extension is described in section 7 of README.TXT.
 
--progress=true
show a progressmeter
 
--gff3=on/off
output in gff3 format
 
--predictionStart=A, --predictionEnd=B
A and B define the range of the sequence for which predictions should be found.
 
--UTR=on/off
predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
 
--noInFrameStop=true/false
Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false
 
--noprediction=true/false
If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
 
--uniqueGeneId=true/false
If true, output gene identifyers like this: seqname.gN
 
--paramlist
Show full list of supported parameters.

AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.