WarpSTR

WarpSTR is an alignment-free algorithm for analysing STR alleles using nanopore sequencing raw reads. The method uses guppy basecalling annotation output for the extraction of region of interest, and dynamic time warping based state automata for calling raw signal data. The tool can be configured to account for complex motifs containing interruptions and other variations such as substitutions or ambiguous bases.

See our preprint at: https://www.biorxiv.org/content/10.1101/2022.11.05.515275v1

Documentation overview

See Installation chapter for information about how to install WarpSTR.

To know more about how to setup the configuration file, see Setting up the config and Advanced parameters. Before running WarpSTR, ensure that input files are located accordingly as set up in the config file.

To know more about output files and what they represent, see Output chapter.

Question

If you have any questions, problems or ideas, please raise an issue on Github or write an email to jozefsitarcik@uniba.sk and we will look further into it as soon as possible.