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Canu — long-read de novo genome assembler for PacBio HiFi, PacBio CLR, and Oxford Nanopore reads. Performs read correction, trimming, and overlap-layout-consensus assembly in three stages. Supports di
Use with AI
Install the MCP server or CLI to instantly fetch Canu documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/canu
dDocent — bash-based RADseq population genomics pipeline for ddRAD, 2bRAD, and ezRAD data. Performs quality trimming (Trimmomatic), de novo or reference-guided assembly (CD-HIT / Rainbow / BWA-MEM), S
2 shared topics • 2 shared operations
Getz Lab tools (ABSOLUTE, MuTect/MuTect2) from the Broad Institute for cancer genomics. ABSOLUTE infers tumor purity, ploidy, and absolute copy numbers from segmented copy number data. MuTect2 (GATK4)
2 shared topics • 1 shared operation
Jellyfish — fast, multi-threaded k-mer counter for DNA sequences. Counts exact k-mer frequencies in FASTA/FASTQ files using a lock-free hash table. Used for genome size estimation (flow cytometry-free
2 shared topics • 1 shared operation
NextDenovo — string graph-based de novo assembler for long reads. Performs error correction (NextCorrect) then assembly (NextGraph) from PacBio CLR, PacBio HiFi, or Oxford Nanopore reads. Config-file
2 shared topics • 1 shared operation
SvABA -- structural variant and indel caller using genome-wide local assembly. Detects deletions, insertions, duplications, inversions, and complex rearrangements from short-read (Illumina) whole-geno
2 shared topics • 1 shared operation