SPAdes

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

The SPAdes tool is available on macOS and Linux operating systems only.

Open Tools ‣ NGS data analysis.

Select the Genome de novo assembly item to use SPAdes.

The Assemble Genomes dialog will appear.

The following parameters are available:

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

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

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 the type and orientation.

Dataset 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.