Skip to main content

Unicycler

alt text

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a short-read-first hybrid assembly.

Requirements

  • Linux or macOS
  • Python 3.4 or later
  • C++ compiler with C++14 support:
    • GCC 4.9.1 or later
    • Clang 3.5 or later
    • ICC also works (though I don't know the minimum required version number)
  • setuptools (only required for installation of Unicycler)
  • For short-read or hybrid assembly:
    • SPAdes v3.14.0 or later (spades.py)
  • For long-read or hybrid assembly:
  • For rotating circular contigs:
    • BLAST+ (makeblastdb and tblastn)

Unicycler expects external tools to be available in $PATH. If they aren't, you can specify their location using Unicycler options (e.g. --spades_path).

alt text

alt text

Figure 1: Key steps in the Unicycler pipeline steps in the Unicycler pipeline.