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MUSET is a software mainly thought for generating an abundance unitig matrix from a collection of sequencing data.

It is optimized for the analysis of multiple FASTA/FASTQ files (gzipped or not).

It includes the following executable:

• muset to build an abundance unitig matrix
• muset_pa to build a presence-absence unitig matrix
• kmat_tools to manipulate/process k-mer matrices

Note: muset only considers "informative" k-mers (i.e., those that are present/absent from a certain number of samples), as opposed to muset_pa which considers all k-mers with multiplicity greater than 1.

Reporting an issue

If you encounter a problem during the execution of MUSET, please open an issue with a description of your run and possibly the log file muset_*.log which is created in the directory from which you ran the pipeline.