spades ☆
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Description:
De novo genome sequence assembly
Type: Formula  |  Latest Version: 4.2.0@0  |  Tracked Since: Oct 12, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics assembly genome spades
Install: brew install spades
About:
SPAdes (St. Petersburg genome assembler) is a de novo genome assembly tool designed for assembling single-cell and standard isolate genomes using short-read sequencing technologies. It employs a multi-Bruijn graph approach to handle repetitive regions and high coverage variation, providing high-quality assemblies for bacterial, fungal, and small eukaryotic genomes.
Key Features:
  • Hybrid assembly support (Illumina + Nanopore/PacBio)
  • Single-cell genome assembly optimization
  • Error correction and repeat resolution algorithms
  • Integrated quality control and validation tools
Use Cases:
  • Bacterial genome assembly from Illumina reads
  • Single-cell microbial genomics
  • Metagenomic assembly (via metaSPAdes mode)
Alternatives:
  • unicycler – Hybrid assembler that wraps SPAdes for short-read assembly
  • megahit – Faster, memory-efficient for metagenomes but less accurate for isolates
  • velvet – Older de Bruijn graph assembler, less sophisticated error handling
Version History
Detected Version Rev Change Commit
Oct 12, 2025 10:23am 0 VERSION_BUMP 84f883d5
Sep 15, 2025 9:45am 0 VERSION_BUMP 53c82187
Sep 13, 2024 10:14pm 0 VERSION_BUMP 4edfe8da
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