Short read de novo assembly with Velevet

Velvet is software to perform dna De novo assembly from short reads by manipulating de Bruijn graphs. Some introduction can be found here: Introduction to de novo assembly with Velvet. It is an old software and recently SPAdes is the most popular de novo assembler. I used Velvet here simply because it is easy to be exported to WebAssembly and it is good enough for simple projects like gene/plasmid assembly.

You can read the Velvet manual or the SPAdes instructions for some parameter setting suggestion.

Recommend using private browser windows to avoid troubles caused by cookies and caches (open from the menu at the topright corner)

No spaces are allowed in input file names!

Step 1: load fastq files and set assembling parameters

Step 2: Start Assembling


  1. velvet:
  2. biowasm project for easy exporting C/C++ tools to WebAssembly.