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Comparative Study
. 2019 Mar 15;35(6):1049-1050.
doi: 10.1093/bioinformatics/bty744.

Large-scale comparative analysis of microbial pan-genomes using PanOCT

Jason M Inman  1 , Granger G Sutton  1 , Erin Beck  1 , Lauren M Brinkac  1 , Thomas H Clarke  1 , Derrick E Fouts  1
Affiliations
Comparative Study

Large-scale comparative analysis of microbial pan-genomes using PanOCT

Jason M Inman et al. Bioinformatics. .

Abstract

Summary: The JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used.

Availability and implementation: Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.

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Figures

Fig. 1.
Fig. 1.
(a) Flowchart diagram of the entire pipeline run by run_pangenome.pl; (b) flowchart diagram of the single-batch processes by run_panoct.pl
See this image and copyright information in PMC

References

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Publication types