Background

HAMLET is a pipeline for analysis of human acute myeloid leukemia RNA-seq samples. Please use the public github repository to open issues or pull requests. It consists of a number of distinct modules, which can be run independently and have their own documentation. Everything is tied together by the main Snakefile using modules.

HAMLET is build to use Singularity or Apptainer to run every Snakemake rule inside its own container. The base execution environment for HAMLET is defined by an environment.yml file.

In addition to the raw output files for each sample, HAMLET also generates a PDF report containing an overview of the essential results. Additional information is available from the summary json file.

Citation

If you use HAMLET in your research, please cite the HAMLET publication.