PGAP specifications


Unique identifier OMICS_10860
Alternative name Prokaryotic Genome Annotation Pipeline
Interface Web user interface
Restrictions to use None
Input data On input, PGAP accepts an assembly (either draft or complete) with a predefined NCBI Taxonomy ID that defines the genetic code of the organism. PGAP also accepts a predetermined clade identifier, matching the genome in question to a species-specific clade.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Mark Borodovsky <>

PGAP articles

PGAP citations

PMCID: 5744436

[…] contigs using spades software v.3.6.2. ( (bankevich et al., 2012). genomes were annotated using the rast annotation system ( and the ncbi prokaryotic genome annotation pipeline ( dna and deduced protein sequences of interest were examined for homology using the on-line blast program […]

PMCID: 5543634

[…] sequence read data were successfully assembled de novo into contigs by using spades version 3.9.0 (6) software., the draft assemblies of the four clinical strains were annotated using the ncbi prokaryotic genome annotation pipeline version 4.1. using bowtie2 version 2.3, we determined that the sequences shared high nucleotide identity (>99%) with the reference genomes of b. melitensis […]

PMCID: 5454195

[…] assemblies were manually analyzed using artemis (2) to correct and trim overlapping sequence on the ends. annotation of the submitted genome assemblies was performed by ncbi staff using the ncbi prokaryotic genome annotation pipeline ( raw pacbio rsii read data have been submitted to the ncbi sequence read archive (sra)., physical mapping […]

PMCID: 5383892

[…] was assessed using quast version 3.1 (5). following trimming, the average length of reads was 245 bp. the genome sequences were annotated using the ncbi prokaryotic genome annotation pipeline (pgap) (6). the statistics for each draft genome sequence are summarized in table 1. comparative analyses of the genome sequences, by average nucleotide identity based on blast (anib) (7), using […]

PMCID: 4919414

[…] os185 (84.94% symmetrical identity and 96.78% gapped identity) (9) among the draft and the complete genome sequences, respectively, in ncbi., the draft genome of strain m1 was annotated using the prokaryotic genome annotation pipeline version 3.1 at ncbi (10). the annotation revealed 4,270 predicted protein-coding sequences, 92 trna genes, and 14 rrna operons., the availability of the genome […]

PGAP institution(s)
National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, GA, USA; School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, USA
PGAP funding source(s)
Intramural Research Program of the NIH National Library of Medicine (in part); NIH grant HG000783 (in part)

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