Example Workflow

A practical example/tutorial can be found in the repository or on the next page.

Although the tool is designed to be flexible and can be used in a variety of ways, it was designed with the following workflow in mind:

1. Have a list of k-mers of interest.
2. Use MerKurio to extract the FASTA/FASTQ records containing these k-mers (and their reverse complements) from the original (paired-end) records.

If sequencing reads were extracted:

3. Align the extracted reads to a reference genome.
4. Use MerKurio to tag the aligned records in a SAM/BAM file with the significant k-mers they contain (and optionally filtering it).
5. Analyzing the matching statistics generated by MerKurio.
6. Interpret the results: e. g., by visualizing the k-mers that are frequently tagged in the reads that align to a particular region of the genome.