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MKMC

MKMC is a multi-stage tool, with variety of functions. Here we give typical scenarios of MKMC running.

Building a matrix and filtering

A typical task includes building a matrix (including filtering k-mers with various criteria). It results in binary .kmcdb and .stats files generation, which may be stored on disk to be utilized later. Matrix building may also generate a text matrix (with normalized or non-normalized counts) and FASTA file with k-mers sequences only. Read more...

Counts normalizing and matrix postprocessing

Postprocessing is aimed at utilizing binary .kmcdb and .stats to create a normalized-counts matrix, and generate various utilitarian results, as correlation, differential k-mers analysis, cross-validation, entropy, dimensionality reduction. Read more...

In all the postprocessing scenarios we expect, that the matrix and additional data are already created in as on Building a matrix and filtering page.

Bulk processing (both matrix building and various postprocessings)

All the abovementioned tasks (matrix building and filtering, and postprocessing) may be peformed together with various configurations. Read more...

Example: revealing sex dimorphism with dimensionality reduction

MKMC may be used to sketch dimorphism of some trait (e.g. sex). The example shows a method of dimensionality reduction running. Read more...

Example: RNA-Seq differential expression patterns determination

MKMC may be used to point out statistically significant k-mers for some design/phenotype, utilizing differential expression algorithms. Read more...