PinAPL-Py

bamutil — C++ toolkit for reading, writing, and manipulating BAM alignment files. Provides duplicate marking (dedup), base quality score recalibration (recab), overlapping read clipping (clipOverlap),

2 shared topics • 2 shared operations

vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,

2 shared topics • 2 shared operations

GREML (GCTA) — genome-based restricted maximum likelihood analysis for SNP heritability estimation, genetic correlation, mixed linear model association (MLMA), and COJO conditional analysis. Use when

2 shared topics • 1 shared operation

GWAS Catalog — EBI/NHGRI curated repository of genome-wide association study summary statistics, significant SNP-trait associations, and ancestry metadata. Query trait-SNP associations, download GWAS

2 shared topics • 1 shared operation

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

2 shared topics • 1 shared operation