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QUAST (Quality Assessment Tool for Genome Assemblies) — evaluate genome assembly quality using contiguity metrics including N50, L50, total length, largest contig, misassemblies, and mismatches. Suppo
Use with AI
Install the MCP server or CLI to instantly fetch QUAST documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/quast
BUSCO (Benchmarking Universal Single-Copy Orthologs) — assess genome assembly, transcriptome, and proteome completeness using lineage-specific single-copy orthologs from the OrthoDB database. Reports
1 shared topic • 2 shared operations
Use when working with gfatools — a lightweight C toolkit for GFA format manipulation — for viewing, converting, sorting, and validating Graphical Fragment Assembly (GFA) files. Provides subcommands fo
1 shared topic • 2 shared operations
Merqury — reference-free quality, completeness, and phasing assessment for genome assemblies using k-mer databases built from Illumina reads. Computes QV (Phred-scaled quality value), k-mer completene
1 shared topic • 2 shared operations
nf-core/mag — Nextflow pipeline for metagenome-assembled genome (MAG) analysis. Takes raw short-read (Illumina) and/or long-read (Nanopore/PacBio) metagenomic sequencing data through quality control,
1 shared topic • 2 shared operations
Purge Haplotigs — pipeline for curating heterozygous diploid genome assemblies by identifying and reassigning haplotigs (alternative haplotype contigs). Analyzes read-depth histograms to set coverage
1 shared topic • 2 shared operations