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+# Some snakemake wrappers to process high throughput sequencing data.
+
+This package provides snakemake wrappers that I use in my high throughput
+sequencing data snakemake workflows.
+
+
+## Installing
+
+Get the source using `git clone
+git@gitlab.pasteur.fr:bli/snakemake_wrappers.git`, `cd` into it and run
+`python3 -m pip install .`
+
+It might also work directly:
+
+    python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/snamemake_wrappers.git
+
+
+Your Python installation should then have a `smwrappers` module available.
+This module's data includes the wrappers.
+
+## Including snakemake wrappers in your snakefile
+
+
+The path to the directory containing the wrappers should be given by the
+`wrappers_dir` object contained in the `smwrappers` module, and can be imported
+as follows:
+
+```{python}
+from smwrappers import wrappers_dir
+```
+
+
+To know which wrappers are available, you can explore the content of this directory.
+For instance:
+
+```{python}
+>>> import os
+>>> from smwrappers import wrappers_dir
+>>> for dir in os.listdir(wrappers_dir):
+...     if not dir.startswith("_"):
+...         print(dir)
+... 
+compute_TPM
+map_on_genome
+intersect_count_reads
+filter_unique_sam
+make_read_stats
+filter_unique_bam
+sam2indexedbam
+feature_count_reads
+filter_size_bam
+compute_RPK
+bigwig_average_over_bed
+bam2fastq
+htseq_count_reads
+```
+
+
+Now you can specify the path to a specific wrapper's directory in the `wrapper`
+directive of a snakemake rule. For instance:
+
+```{python}
+    wrapper:
+        f"file://{wrappers_dir}/map_on_genome"
+```
+
+To know precisely how to interface a given wrapper with your rule, you need to
+look at the code contained in the `wrapper.py` file contained in the wrapper's
+directory. The `snakemake` object represents the rule, and has attributes such
+as `input`, `output`, `params`, `threads`, and may sometimes also access to
+information defined in the `config` dictionary via `snakemake.config`.
+
+
+## Citing
+
+If you use this package, please cite the following paper:
+
+> Barucci et al, 2020 (doi: [10.1038/s41556-020-0462-7](https://doi.org/10.1038/s41556-020-0462-7))