Large-scale comparative analysis of microbial pan-genomes using PanOCT.
Bioinformatics
; 35(6): 1049-1050, 2019 03 15.
Article
en En
| MEDLINE
| ID: mdl-30165579
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Genoma Bacteriano
/
Genoma Microbiano
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2019
Tipo del documento:
Article
País de afiliación:
Estados Unidos