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Use when working with vg — the variation graph toolkit — for pangenome graph construction, read mapping to variation graphs, and graph-aware variant calling. Builds genome graphs from VCF + reference
Use with AI
Install the MCP server or CLI to instantly fetch vg documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/vg
docker pull biocontainers/vg:1.70.0BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace
1 shared topic • 3 shared operations
LSHTM PathogenSeq bioinformatics pipelines for pathogen whole-genome sequencing analysis, including TB-Profiler for Mycobacterium tuberculosis lineage and drug-resistance prediction from WGS data, Mal
1 shared topic • 3 shared operations
Snippy — rapid haploid variant calling pipeline for bacterial genomics. Maps paired-end or single-end reads to a reference genome using BWA-MEM and Minimap2, calls SNPs, MNPs, and indels via Freebayes
1 shared topic • 3 shared operations
GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-
1 shared topic • 2 shared operations
OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se
1 shared topic • 2 shared operations