Medaka

SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno

2 shared topics • 3 shared operations

Broad Institute tools — access Terra cloud genomics platform, GSEA/MSigDB gene set enrichment analysis, GenePattern workflow server, Picard sequencing utilities, and FireBrowse TCGA data portal progra

3 shared topics • 1 shared operation

Maftools — R package for analyzing somatic mutations from cancer sequencing (MAF files). Provides oncoplots for mutation visualization, clonality analysis, tumor burden estimation, mutational signatur

3 shared topics • 1 shared operation

Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal

2 shared topics • 2 shared operations

sigmap is a C++ tool for signal-level alignment of nanopore sequencing data, mapping raw electrical signals (squiggles) directly to a reference genome without basecalling. Uses Dynamic Time Warping (D

2 shared topics • 2 shared operations