S3A

S3A (Scalable and Accurate Annotated Assembly) is a fast and accurate gene-targeted assembler based on the Overlap-Layout Consensus paradigm to reconstruct coding regions from domain annotated metagenomic sequence reads.

S3A is made available on the UFS HPC via a conda environment which can by loaded as a module.

UFS HPC Usage Example

Follow these steps to use S3A:

  1. Start a qwiz or qvnc session. If using a qvnc session, open the Terminal.

  2. Load the S3A module (current version is 1.0): 

    $ module load life-sciences/S3A

  3. Initialize the S3A environment: 
    $ S3A_init
  4. S3A can now be executed as follows: 
    $ S3A_Assembler.py  *add arguments here*

Note

The applications bcalm , fraggenescan and hmmer are needed to prepare the input for S3A and have been installed inside the environment. Consult the manual for instructions on how to use them to prepare the input

  • 1 Node
  • Memory and number of cores will depend on dataset size

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

  • No community guides are available.

Official site and documentation

Licensing Information

  • S3A is freely available for download and use, however no licensing information is provided beyond this.

Primary citation

L. David, R. Vicedomini, H. Richard, and A. Carbone. "Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A." Bioinformatics 2020.

Please remember to cite any additional methods used.

External Guides and Resources

  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za