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Use when working with viral-ngs, Broad Institute viral genomics tooling, viral sequencing pipelines, pathogen read depletion, metagenomic classification, viral assembly, or intrahost/interhost variant
Use with AI
Install the MCP server or CLI to instantly fetch viral-ngs documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/viral-ngs
nf-core/viralrecon — Nextflow pipeline for viral genome reconstruction and analysis from sequencing data. Supports Illumina and Oxford Nanopore reads for SARS-CoV-2, influenza, and other viral genomes
3 shared topics • 2 shared operations
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
3 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
3 shared topics • 1 shared operation
PrimerBLAST is an NCBI web tool that combines Primer3 for PCR primer design with BLAST-based specificity checking against NCBI databases. Designs primers for a target sequence, checks them for off-tar
3 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,
3 shared topics • 1 shared operation