VarDict

Use when working with the ARTIC viral amplicon sequencing command-line pipeline for Oxford Nanopore data. Covers documented `artic minion`, `artic guppyplex`, and `artic_get_models` workflows for prim

2 shared topics • 1 shared operation

CNVkit -- Python toolkit for detecting copy number variants (CNVs) from targeted DNA sequencing data (hybrid capture, amplicon) and whole-genome sequencing (WGS). Leverages both on-target and off-targ

2 shared topics • 1 shared operation

DADA2 — high-resolution amplicon sequence variant (ASV) inference from Illumina, 454, and Ion Torrent amplicon sequencing data. R/Bioconductor package that models sequencing errors to resolve exact bi

2 shared topics • 1 shared operation

Use when working with iVar for viral amplicon sequencing, primer trimming, intrahost variant calling, consensus generation, replicate-aware variant filtering, or primer mismatch masking workflows. iVa

2 shared topics • 1 shared operation

VarScan2 -- Java-based variant caller for somatic and germline SNV/indel detection, copy number analysis, and LOH detection from samtools mpileup output. Supports tumor-normal paired somatic calling,

2 shared topics • 1 shared operation