Introduction

MerKurio was developed as command line tool and provides two main functionalities through dedicated subcommands.

The extract subcommand identifies and extracts sequence records from fasta or fastq files based on query k-mers, with full support for paired-end reads where matching in one read extracts both mates.

The tag subcommand annotates sequences in SAM or BAM alignment formats according to the k-mers that they contain following the SAM Optional Fields Specification with user-defined labels (default “km”).

It was developed to sinmplify downstream analysis of selected k-mers by tracing them back to their sequences in the original data.

For installation instructions, go to the installation section.

To test MerKurio on a minimal working example, visit the minimal example section.

For an example workflow, visit the practical tutorial section.

You can use the search bar on top to find specific information, or use the navigation on the left to browse the manual.

If you have found a bug or have a feature request, please open an issue on the GitHub repository or check the discussions on GitHub.

License

The code in this repository is licensed under the MIT license.

Test data and example files in the tests/ and example-minimal/ directories are licensed under the CC0 1.0 Universal license.