Flye — de novo assembler for single-molecule sequencing reads (PacBio CLR, PacBio HiFi, Oxford Nanopore) using repeat graphs built on approximate sequence matching. Produces polished contigs, GFA repe
Use with AI
Install the MCP server or CLI to instantly fetch Flye documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/flye
docker pull biocontainers/flye:unknownCanu — 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