Creation of a SNAP model from BUSCO output.
Using MAKER's cegma2zff as archetype, busco2snap.pl creates a SNAP model from complete, single-copy BUSCOs by predicting the gene structure with the retrained Augustus model and converting to zff format. The tools augustus and blastp need to be in your $PATH. If fathom, forge and hmm-assembler.pl are in your $PATH the SNAP model will be created automatically.
If Augustus predicts more than one gene at a BUSCO locus, the predicted proteins are blasted against the ancestral variants of the corresponding BUSCO lineage. The gene(s) where the best hit (defined by highest bit score) is on the searched BUSCO are used only.
busco2snap.pl needs the following Perl modules and will search for executables in your $PATH:
Mandatory:
- Parallel::Loops
- Augustus:
augustus - BLAST+:
blastp
Optional:
- SNAP:
fathom,forge,hmm-assembler.pl
busco2snap.pl -b <busco_dir>
Mandatory:
-b STR BUSCO output directory (run_*)
(augustus_output/retraining_parameters/)
Options: [default]
-dup Include duplicated BUSCOs [off]
-frag Include fragmented BUSCOs [off]
-o STR Output directory [.]
-pre STR Prefix for file name of the SNAP model file [species model name]
-t INT Number of parallel processed BUSCOs [1]
-kt Keep temporary files [off]
-v Print executed commands to STDERR [off]
-dry-run Only print commands to STDERR instead of executing [off]
-h or -help Print this help and exit
-version Print version number and exit
If you use this tool please cite the dependencies:
- Augustus:
Stanke M, Steinkamp R, Waack S, Morgenstern B (2004). AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Research, 32(suppl_2):W309–W312, https://doi.org/10.1093/nar/gkh379 - BLAST+:
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10(1):421, https://dx.doi.org/10.1186%2F1471-2105-10-421 - SNAP:
Korf I (2004). Gene finding in novel genomes. BMC Bioinformatics, 5(1):59, https://doi.org/10.1186/1471-2105-5-59