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PGAP specifications


Unique identifier OMICS_08611
Alternative names Pan-Genome Analysis Pipeline, NCBI_PGAP
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Jun Yu

Publication for Pan-Genome Analysis Pipeline

PGAP citations


Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake

Genome Announc
PMCID: 5876485
PMID: 29599156
DOI: 10.1128/genomeA.00190-18

[…] s were predicted by using IslandViewer 4.0 (), prophages by using PHASTER (), and clustered regularly interspaced short palindromic repeats (CRISPRs) by using CRISPRfinder ().Genome annotation by the NCBI PGAP predicted 4,117 genes, including 4,026 coding sequences (CDSs), while RNA genes were composed of 11 rRNAs and 75 tRNAs. The genome of B. paralicheniformis F47 exhibits 99.26% ANI, 0.94 AF, a […]


The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow

Microb Genom
PMCID: 5885020
PMID: 29583117
DOI: 10.1099/mgen.0.000169
call_split See protocol

[…] idated against Jspecies coverage results; these are interactive, but hard to tabulate for all genome pairs. The pairwise homoplasy index [] was used as the intragene recombination test and was run on PGAP-defined [] and mafft-aligned [] core genes of ANI-delineated bacteriophage groups. PGAP takes as input a complete set of predicted proteins and genes of all the genomes in a sample and performs a […]


Complete Genome Sequence of the Symbiotic Strain Bradyrhizobium icense LMTR 13T, Isolated from Lima Bean (Phaseolus lunatus) in Peru

Genome Announc
PMCID: 5843721
PMID: 29519840
DOI: 10.1128/genomeA.00146-18
call_split See protocol

[…] (). Assembly reconciliation was performed by mapping reads over sequence differences and manually correcting possible errors or misassemblies. Gene prediction and annotation were performed using the NCBI PGAP ().The genome of LMTR 13T was composed of single circular chromosome of 8,322,773 bp with a G+C content of 62%. The numbers of predicted coding sequences (CDSs) and tRNA genes were 7,456 and […]


Piggy: a rapid, large scale pan genome analysis tool for intergenic regions in bacteria

PMCID: 5890482
PMID: 29635296
DOI: 10.1093/gigascience/giy015

[…] a careful consideration of gene presence and absence alongside gene regulation. Here, we address this by introducing a new pipeline called Piggy that closely emulates and complements the established pan-genome analysis pipeline Roary []. Input and output files for Piggy and Roary use the same format and run in a similar time on modest computing resources. Piggy provides a means to rapidly identif […]


Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

Front Microbiol
PMCID: 5817063
PMID: 29491851
DOI: 10.3389/fmicb.2018.00184

[…] eads 17 kilo base (kb) and above. Contigs were polished using Quiver and annotation was performed via Rapid Annotation using Subsystem Technology (RAST v2.0) or Prokaryote Genome Annotation Pipeline (PGAP v4.2.) (Zhao et al., ; Overbeek et al., ). […]


Genomic Architecture of the Two Cold Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

Genome Biol Evol
PMCID: 5833320
PMID: 29438502
DOI: 10.1093/gbe/evy029

[…] irst approach, a clustering based on the neighbor-joining model was performed to compare the DNA sequence of the genes from the core genome. The core genome and the distance matrix were calculated by PGAP v.1.11 () using a coverage cutoff of 80% and identity of 50%. The output file 4.PanBased.NJ.tree was analysed in the software SplitsTree v.4.14.2 () to obtain an unrooted tree. In the second appr […]


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PGAP institution(s)
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
PGAP funding source(s)
National Basic Research Program (973 Program) (No. 2010CB126604); Special Foundation Work Program (No. 2009FY120100), Ministry of Science and Technology of the People's Republic of China; National Science Foundation of China (No. 31071163)

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