DYNAMITEDYNAMITE is a pure-Rust ORF and gene caller for phages, viruses, giant viruses, crassphages, bacteria, archaea, eukaryotes, metagenomic contigs, and raw sequencing reads. It provides a single command-line interface to PHANOTATE-, Prodigal-, Prodigal-GV-, Prodigal-meta-, GeneMark-, AUGUSTUS-, and FragGeneScan-based gene-calling engines, with automatic organism-mode and genetic-code selection.Versions

v1.0.0 (default)

Tags: gene prediction, ORF calling, genome annotation, phage, virus, metagenomics, RustParameters

input (file) required: Input nucleotide FASTA containing assembled contigs, genomes, short reads, or long reads. Gzip-compressed FASTA is supported.

mode (enum) required: Organism/input mode. DYNAMITE uses this to select an appropriate gene-calling engine and genetic code. Options: auto, phage, virus, giant-virus, crassphage, bacteria, archaea, meta and 3 more

engine (enum): Optional gene-calling engine override. When unset, the engine is selected from the organism mode. Options: phanotate, prodigal, prodigalgv, prodigal-meta, genemark, augustus, fraggenescan

genetic_code (str): Optional NCBI translation-table number, such as 11, 4, 15, or 25, or 'auto' for automatic detection. When unset, the selected mode determines the default.

closed (bool): Require complete genes and exclude gene calls that run off the ends of contigs.

minlen (int): Minimum ORF length in nucleotides. This option applies to the PHANOTATE engine. A value of 0 leaves DYNAMITE's normal behavior unchanged.

Links

Home page

Documentation

GitHub repository

License: CC BY-NC 4.0

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