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.