Augustus
Augustus is a program to find genes and their structures in one or more genomes.[1][2]
Installed Version
Augustus 3.4.0 is installed on Picotte as a Singularity container. Use the modulefile:
augustus/3.4.0
Running
To run the example, first clone the Augustus repo:
[juser@picotte001 myrsrchGrp]$ git clone https://github.com/Gaius-Augustus/Augustus.git
[juser@picotte001 myrsrchGrp]$ cd Augustus
Then, create this example job script, naming it "testaugustus.sh":
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=64GB
module load augustus/3.4.0
singularity run --bind /ifs/groups/myrsrchGrp/Augustus:/temp $AUGUSTUSDIR/augustus.sif augustus --species=human --UTR=on /temp/examples/example.fa
And submit it as usual:
[juser@picotte001 Augustus]$ sbatch testaugustus.sh
This run should take several seconds. The expected output is:
# This output was generated with AUGUSTUS (version 3.4.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM
# Initializing the parameters using config directory /opt/augustus-3.4.0/config/ ...
# human version. Using species specific transition matrix: /opt/augustus-3.4.0/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like examples/example.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
HS04636 AUGUSTUS gene 836 8857 1 + . g1
HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1
HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/10
# CDS introns: 0/9
# 5'UTR exons and introns: 0/1
# 3'UTR exons and introns: 0/1
# hint groups fully obeyed: 0
# incompatible hint groups: 0
# end gene g1
###
#
# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
#
# Predicted genes for sequence number 2 on both strands
# start gene g2
HS08198 AUGUSTUS gene 86 2344 1 + . g2
HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1
HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/5
# CDS introns: 0/5
# 5'UTR exons and introns: 0/1
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 0
# end gene g2
###
# command line:
# augustus --species=human --UTR=on examples/example.fa
Reference
[1] Augustus GitHub repository
[2] Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24(5), pages 637–644, doi: 10.1093/bioinformatics/btn013