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megahit

The premium Open Source alternative to Illumina BaseSpace

🎯 Best for:Large-scale metagenomic assembly on limited hardware
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GPL-3.0License

What is megahit?

Replaces proprietary metagenomic assemblers for large-scale environmental sequencing data. Utilizes succinct de Bruijn graphs to achieve ultra-low memory footprints during contig assembly.

Tech Stack
C++Biology & Biotechnology

Why megahit?

  • • Extremely memory efficient
  • • Supports co-assembly of multiple samples
  • • Highly scalable on HPC clusters

Limitations

  • • CLI only interface
  • • Limited visualization tools
  • • Steep learning curve for beginners
3/4/2026
Last Update
140
Forks
107
Issues
GPL-3.0
License
Financial Leak Detected

Stop the "SaaS Tax"

Your team could be burning cash. Switching to megahit instantly boosts your runway.

Competitor Cost
-$1,440
/ year (est. based on Illumina BaseSpace)
Self-Hosted
$0
/ year
Team Size10 Users
150+
Launch Detailed Calculator
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