KING

Use when working with bigsnpr — an R package for analysis of massive

1 shared topic • 2 shared operations

Nextclade — viral genome alignment, clade/lineage assignment, mutation calling, and sequence quality assessment. Aligns query sequences against pathogen-specific reference datasets (SARS-CoV-2, influe

1 shared topic • 2 shared operations

Nextclade CLI — viral genome quality control, clade assignment, mutation calling, and phylogenetic placement for SARS-CoV-2, influenza (H3N2, H1N1, H5N1), RSV, mpox, and 100+ other pathogen datasets.

1 shared topic • 2 shared operations

Peddy — pedigree and sample QC tool for VCF files. Verifies sample sex from X-chromosome heterozygosity, checks relatedness against PED file expectations, predicts ancestry via PCA against 1000 Genome

1 shared topic • 2 shared operations

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

1 shared topic • 2 shared operations