prodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Python3 wrapper for parallelized gene prediction using Prodigal

De novo genome assembly and structural annotation of bacterial isolate SRR25083113 using SPAdes, Prodigal, Barrnap, and ARAGORN — a macOS ARM–compatible pipeline alternative to QUAST/Prokka.

Unified bacterial genome QC: BUSCO-style completeness, contamination detection that tells plasmids from contaminants, and comparative gene content with a permutation null for genomic islands.

Pipeline to fetch species assemblies from NCBI, run MacSyFinder per genome, and emit clean system/component matrices.

The current code I developed to compare the examples programs

Projeto elaborado para WBDS LA CAMP- Anotação do genoma da bactéria Clostridium botulinum com pyrodigal e prokka

Bakta and Prokka call the same 87,859 CDS regions in 25 complete bacterial genomes, then give 51.7% of them different product names. Both wrap Prodigal, so they agree on gene boundaries and diverge on function. Grouped-by-genome ML shows the disagreement tracks database coverage, not sequence.

Comprehensive three-way consensus annotation pipeline for Giardia genomes (v5.0)