ArticleFunctional & integrative genomics2026
An optimized and integrated robust tool for pangenome generation.
Article in Functional & integrative genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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6 authors.
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Abstract
Graph based pangenomes approaches represent a highly effective framework for clustering and comparative analysis of genomes across different subspecies. Traditionally, generating a complete pangenome involves the use of multiple subpackages, understanding of optimization in the light of time and memory complexity and a firm grasp on Linux based command line programming. To address and transform the multi-step command line process into a user-friendly approach, a software package was designed to integrate and automate all the steps involved − (1) genome annotation, (2) gene completeness statistics, (3) gene family cluster simplification and (4) genome-to-gene mapping. The designed package boasts improved memory footprint and runtime optimizations by implementing parallelization of processes, achieving a speedup of 2.53x when implemented on a test set of 150 genomes. To demonstrate its functionality and validate its accuracy, the tool was used as a test case to generate a pangenome and analyze genomes of Geobacillus species. The genomes chosen in the final pangenome were curated based on the metrics of CheckM Completeness and BUSCO (Benchmarking Universal Single-Copy Orthologs) scores. Annotation of the genomes was performed by PROKKA and then clustered by PPanGGOLiN. Post-processing modules for Gene Ontology and UniProt analysis are also included. The entire software package was designed in a modular fashion - to allow users the option to switch out modules for either ones designed by themselves or ones tailored to their requirements.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.