flye ☆
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Description:
De novo assembler for single molecule sequencing reads using repeat graphs
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics assembly long-read nanopore
Install: brew install flye
About:
Flye is a de novo assembler specifically designed for long, noisy reads from single-molecule sequencing technologies like PacBio and Oxford Nanopore. It constructs assembly graphs to resolve repeats and structural variations, producing highly contiguous assemblies even for complex genomes. This makes it a critical tool for assembling genomes that are difficult to map with short-read data.
Key Features:
  • Handles raw reads without error correction
  • Specialized for PacBio and Oxford Nanopore data
  • Capable of assembling repetitive and complex regions
  • Outputs assembly graphs for structural analysis
Use Cases:
  • De novo genome assembly from long-read sequencing data
  • Structural variant detection in complex genomes
  • Assembling organellar genomes and plasmids
Alternatives:
  • Canu – Canu includes a correction step, whereas Flye works directly on raw reads, often making Flye faster but potentially less accurate on high-error data.
  • SPAdes – SPAdes is optimized for hybrid or short-read assembly, while Flye is purpose-built for single-molecule long reads.
Version History
Detected Version Rev Change Commit
Sep 26, 2025 10:11pm 0 VERSION_BUMP 30a908d2
Sep 26, 2025 12:05pm 0 VERSION_BUMP 8951738f
Sep 13, 2025 5:44pm 0 VERSION_BUMP c9864a0c
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