The automatic prokaryotic genome annotation pipeline for Genome Warehouse, based on NCBI's Prokaryotic Genome Annotation Pipeline (PGAP), is designed to streamline the annotation process of prokaryotic genomes. This pipeline integrates various computational tools to analyze genomic sequences, predict gene features, and classify functional annotations automatically. It processes raw genomic sequences by identifying coding regions, non-coding elements, and potential genomic features, ultimately generating comprehensive annotation reports. This automation enhances efficiency, accuracy, and scalability, enabling researchers to focus on downstream analysis and interpretation of genomic data.

We evaluated the quality of reannotation using CheckM. As of Oct. 27, 2024, we have found 41 genome assemblies with user submitted annotations among all 3925 GWH prokaryotic genome assemblies (Figure 1). The evaluation results of checkM show that the completeness of 41 PGAP reannotation results is around 94.18% (±7%), and the contamination rate is around 2.2% (±1.87%). The completeness of the 41 user-submitted genome annotation is around 91.72% (±10.25%), and the contamination rate is around 1.28% (±1.27%). Those data shows that the quality of the two gene structure annotations is both high. And in many cases, there is no significant improvement for PGAP reannotation. However, the improvement of reannotation resource is mainly reflected in the following points: (1) The incorporation of NCBI PGAP to GWH serves as a uniform and standardized pipeline and provides high-quality genome annotations to those assemblies that do not have an annotation (from 0.014% to 92.44%); (2) Besides protein-coding genes, GWH reannotation provides ncRNA, CRISPR elements and fast evolving genes annotations (from 0.008% to 92.44%); (3) In addition, GWH reannotation can also provide identification of pseudogenes (from 0.0002% to 92.44%). (4) Besides gene structure, it provides gene function annotation (from 0.008% to 92.44%). Those improvements will help the users to utilize the genome assembly data and promote genomic research.

Figure 1 The comparison of PGAP annotations and user-submitted annotations on the same 41 genome sequences.