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

Open Tools ‣ DNA assembly.

     <img src="/wiki/download/attachments/14057535/SPAdes.png"/>

Select the Assemble genomes item to use the SPAdes.

The Assemble Genomes dialog will appear.

     <img src="/wiki/download/attachments/14057535/SPAdes_1.png"/>

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.