SPAdes – St. Petersburg genome assembler. Click this link  to open SPAdes homepage. SPAdes is embedded as an external tool into UGENE.

Open Tools ‣ NGS data analysis.

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Select the Genome de novo assembly item to use the SPAdes.

The Assemble Genomes dialog will appear.

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The following parameters are available:

Output directory - SPAdes stores all output files in output directory, which is set by the user.

Library - to run SPAdes choose one of the following libraries:

• • Single-end
  • Paired-end
  • Paired-end (Interplaced)
  • Paired-end (Unpaired files)
  • Sanger
  • PacBio

Left reads -  file(s) with left reads. 

Right reads -  file(s) with right reads.

 For each dataset  in the paired-end libraries you can change type and orientation.

Datasest type - dataset type.

Running mode - running mode.

k-mer sizes (-k) - k-mer sizes.

Number of threads (-t) - number of threads.

Memory limit GB (-m) - memory limit.