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PGAP

NCBI Prokaryotic Genome Annotation Pipeline

The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs and pseudogenes.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Pipeline was developed in 2001 and is regularly upgraded to improve structural and functional annotation quality (Li W, O'Neill KR et al 2021). Recent improvements include utilization of curated protein profile hidden Markov models (HMMs), and curated complex domain architectures for functional annotation of proteins and annotation of Enzyme Commission numbers and Gene Ontology terms. Post-annotation, the completeness of the annotated gene set is estimated with CheckM.

The workflow provided here also offers the option to confirm or correct the organism associated with the genome assembly prior to starting the annotation, using the Average Nucleotide Identity tool.

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Need to assemble the genome too? Use RAPT for producing an annotated genome starting from short reads