Loading homepage
MEGAHIT — ultra-fast and memory-efficient NGS assembler for large and complex metagenomes, single genomes, and single-cell data. Uses succinct de Bruijn graph (SdBG) with an iterative multi k-mer stra
Use with AI
Install the MCP server or CLI to instantly fetch MEGAHIT documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/megahit
Use when working with Jovian for viral metagenomics or viromics from raw paired-end Illumina FASTQ data in public-health, clinical, or batch sequencing contexts. Jovian is a Snakemake-based workflow t
2 shared topics • 1 shared operation
metaSPAdes — de novo metagenomic assembler from the SPAdes suite using iterative de Bruijn graphs with multiple k-mer sizes optimized for uneven-coverage metagenomes. Assembles short-read (Illumina pa
2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation
ShortBRED — metagenomics protein-family quantification tool from the bioBakery suite. Identifies short, representative peptide markers from protein families and quantifies their relative abundance in
2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation