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Shasta — fast de novo long-read genome assembler optimized for Oxford Nanopore (ONT) reads. Produces haploid or phased diploid assemblies from nanopore data using run-length encoding, MinHash-based ov
Use with AI
Install the MCP server or CLI to instantly fetch Shasta documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/shasta
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
2 shared topics • 1 shared operation
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