GSMR

AGAT (Another Gff Analysis Toolkit) — comprehensive Perl toolkit for reading, writing, validating, fixing, and manipulating genome annotation files in GFF3, GTF, and GFF2 formats. Converts between for

2 shared topics • 1 shared operation

Meryl — fast k-mer counting and set-operation toolkit from the Marbl group (Canu/Verkko). Counts canonical or strand-specific k-mers from FASTA/FASTQ inputs into binary meryl databases, then supports

2 shared topics • 1 shared operation

PLINK 1.9/2 — high-performance command-line toolset for whole-genome association analysis, population stratification, identity-by-descent, linkage disequilibrium computation, and genotype data managem

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

VCFtools — C++ toolkit for filtering, comparing, summarizing, converting, and manipulating VCF (Variant Call Format) and BCF files. Provides site and individual-level filtering, allele frequency calcu

2 shared topics • 1 shared operation