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=hintsfilename
           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 "SAMPLING: ALTERNATIVE TRANSCRIPTS AND POSTERIOR
           PROBABILITIES" of docs/RUNNING-AUGUSTUS.md.

       --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 "AUGUSTUS-PPX" of docs/RUNNING-AUGUSTUS.md.

       --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/doc/augustus/README.md.gz.

                                                                                                     AUGUSTUS(1)