Gubbins

Roary — rapid large-scale prokaryotic pan genome analysis. Calculates the pan genome from annotated assemblies (GFF3 from Prokka/Bakta), producing core and accessory gene clusters, gene presence/absen

3 shared topics

GWAS Catalog tools (gwas-sumstats-tools) are EMBL-EBI utilities for reading, writing, validating, and formatting genome-wide association study (GWAS) summary statistics in the GWAS-SSF standard format

2 shared topics • 1 shared operation

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

2 shared topics • 1 shared operation

RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

2 shared topics • 1 shared operation

snpStats is an R/Bioconductor package for GWAS (genome-wide association study) and population genetics analysis. It provides SnpMatrix and XSnpMatrix objects for efficient SNP data storage, PLINK bina

2 shared topics • 1 shared operation