evidencemodeler
Link to section 'Introduction' of 'evidencemodeler' Introduction
Evidencemodeler is a software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.
For more information, please check its website: https://biocontainers.pro/tools/evidencemodeler and its home page on Github.
Link to section 'Versions' of 'evidencemodeler' Versions
- 1.1.1
Link to section 'Commands' of 'evidencemodeler' Commands
- evidence_modeler.pl
- BPbtab.pl
- EVMLite.pl
- EVM_to_GFF3.pl
- convert_EVM_outputs_to_GFF3.pl
- create_weights_file.pl
- execute_EVM_commands.pl
- extract_complete_proteins.pl
- gff3_file_to_proteins.pl
- gff3_gene_prediction_file_validator.pl
- gff_range_retriever.pl
- partition_EVM_inputs.pl
- recombine_EVM_partial_outputs.pl
- summarize_btab_tophits.pl
- write_EVM_commands.pl
Link to section 'Module' of 'evidencemodeler' Module
You can load the modules by:
module load biocontainers
module load evidencemodeler
Link to section 'Example job' of 'evidencemodeler' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Evidencemodeler on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=evidencemodeler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers evidencemodeler
evidence_modeler.pl --genome genome.fasta \
--weights weights.txt \
--gene_predictions gene_predictions.gff3 \
--protein_alignments protein_alignments.gff3 \
--transcript_alignments transcript_alignments.gff3 \
> evm.out