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# 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. K├Ânig, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

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