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Velvet — de Bruijn graph short-read genome assembler for Illumina, Solexa, and 454 sequencing data. Runs as a two-stage pipeline: velveth builds the hash table and de Bruijn graph, velvetg traverses t
Use with AI
Install the MCP server or CLI to instantly fetch Velvet documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/velvet
PacBio Revio tools — suite of command-line utilities for processing HiFi long reads generated by the PacBio Revio system. Covers CCS (circular consensus sequencing) generation with pbccs/ccs, demultip
3 shared topics
Use when building, querying, or manipulating colored compacted de Bruijn graphs (ccDBG) with Bifrost for genome assembly, metagenomics, variant detection, or k-mer analysis. Covers graph construction
2 shared topics • 1 shared operation
DAS Tool — genome-resolved metagenomics bin refinement tool that integrates results from multiple binning algorithms to produce an optimized, non-redundant set of metagenome-assembled genomes (MAGs).
2 shared topics • 1 shared operation
In-silico PCR (isPCR) simulates PCR amplification computationally by searching a genome or sequence database for products defined by primer pairs. Use for primer specificity checking, amplicon predict
2 shared topics • 1 shared operation
Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch
2 shared topics • 1 shared operation