superSTR

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.

The C99 component of superSTR uses and incorporates a modified version of mreps by Roman Kolpakov, Ghizlane Bana and Gregory Kucherov. Full details of mreps can be found at http://mreps.univ-mlv.fr/ and in its accompanying paper; R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acid Research, 31 (13), July 1 2003, pp 3672-3678.

Full details of libraries used in superSTR can be found in the Acknowledgements file.

Basic superSTR operations

This section describes how to run basic superSTR analysis with a minimum of fuss on human genomic samples.

Installing superSTR

1) Processing FASTQs and BAM files 2) Post-processing of sets of samples 3) Outlier detection 4) Motif screening 5) Visualisation

We also provide a detailed example RNA-seq analysis based on the SCA3 data used in the superSTR manuscript to illustrate an end-to-end superSTR analysis.

Upcoming changes:

• A few modifications to improve UI in the code will be implemented to standardise flags across utilities.
• mreps' resolution parameter will be exposed to the user in the next update.

Licensing

superSTR is released under the GNU General Public License, v2.

Acknowledgements:

• @jbedo for bugfixes and helping streamline the Cmake files used to compile superSTR.
• @christopher-schroeder for developing conda installation methods for superSTR and bugfixes.