AUGUSTUS-Teaching

Category

Bioinformatics

Program On

Teaching

Version

3.2.3

Author / Distributor

AUGUSTUS

Description

"AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" More details are at AUGUSTUS

Running Program

The last version of this application is at /usr/local/apps/eb/AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14

To use this version, please load the module with

ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_AUGUSTUS
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=AUGUSTUS.%j.out
#SBATCH --error=AUGUSTUS.%j.err

cd $SLURM_SUBMIT_DIR
ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14
augustus [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14 
augustus 
AUGUSTUS (3.2.3) is a gene prediction tool
written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

usage:
augustus [parameters] --species=SPECIES queryfilename

'queryfilename' is 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.

parameters:
--strand=both, --strand=forward or --strand=backward
--genemodel=partial, --genemodel=intronless, --genemodel=complete, --genemodel=atleastone or --genemodel=exactlyone
  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
--sample=n
--minexonintronprob=p
--minmeanexonintronprob=p
--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

For a complete list of parameters, type "augustus --paramlist".
An exhaustive description can be found in the file README.TXT.

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Installation

Source code is obtained from AUGUSTUS

System

64-bit Linux