SKESA (citation) is a de novo assembler for Illumina whole genome read data. It can be used in the assembling pipeline if the SeqSphere+ client is running on Linux or if the Windows Subsystem for Linux is installed on Windows.

SKESA is De Bruijn graph-based and designed for assembling reads of microbial genomes sequenced using Illumina. It is not suited for assembling data from Ion Torrent or 454 machines.

See the page Assembler Evaluation for a detailed comparison of the performance of SKESA, SPAdes, and Velvet.

Quality Trimming

SKESA parameters dialog in pipeline script

SKESA performs a trimming of the read data. Therefore, it is not recommended to use the SeqSphere+ read trimming as pre-processing (disabled by default).


To reduce the size of the output files and the time and memory consumption, the input files can be downsampled. Downsampling randomly removes reads so that the given approximate coverage is obtained. If quality trimming is selected, downsampling is done on the trimmed reads. By default downsampling to 180x coverage is enabeled. However, downsampling can be disabled or the coverage can be changed if wished.


By default a remapping is performed in a pipeline that uses SKESA with the default settings. After the SKESA process has finished, BWA is used to align the reads against the resulting assembly contigs. BWA mem is used as algorithm and for the resulting alignment (BAM file) a new consensus is called. For the consensus calling procedure no threshold for minimum coverage is set. The required read support for a consensus base is 60%.

SKESA Options

The number of cores (by default all) and the maximum amount of memory that should be used can be specified here. Furthermore, additional command line parameters for SKESA can be defined here (see SKESA manual).

If SKESA was used in a pipeline, then the logging output of SKESA can later be viewed in the Procedure tab of the finished Sample.

SKESA Version

By default, the SKESA version in the subdirectory ext/ of the SeqSphere+ Client installation directory is used (version 2.4.0). In the Advanced Settings of SKESA in the pipeline script an alternative version can be defined.

However, SeqSphere+ is only tested with the SKESA version that is delivered with the software. SKESA may be updated with future SeqSphere+ updates.