Added documentation.

README.md

+# Barcode: Design NGS barcodes
+Barcode is a program for the design and validation of sets of barcodes.
+
+Barcodes are used in NGS to tag samples before pooling. After sequencing, these
+barcodes are used to *demultiplex* the data, thereby assigning the reads to the
+originating sample.
+
+The key aspect of a good set of barcodes is robustness against read errors. One
+read error should not be able to transform one barcode into another. This
+requirement can be met by selecting barcodes in such a way that the *edit
+distance* between any pair of barcodes is larger than one. An additional
+desired property is the ability to *correct* read errors. This can be done by
+increasing the minimal edit distance between barcodes to at least three. If one
+read error occurs, the sequenced barcode will have a distance of one to the
+original barcode and a minimum distance of two to any of the other barcodes. If
+the read error is high, the minimum edit distance should be increased to a
+higher (odd) number.
+
+For some sequencers it is important that mononucleotide stretches in barcodes
+are below a minimum length. An additional filter can be used to remove these
+barcodes.
+
+Development of Barcode is hosted
+[on our GitLab server](https://git.lumc.nl/j.f.j.laros/barcode).
+
+## Easy installation
+If you have installed the `pip` package installer, you can easily install
+Barcode by typing:
+
+    pip install barcode
+
+## Installing from source
+To install from the source repository, use:
+
+    git clone https://git.lumc.nl/j.f.j.laros/barcode.git
+    cd barcode
+    pip install .
+
+## Usage
+The `barcode` program has two subcommands; one for the creation of a set of
+barcodes and one for the validation of an existing set of barcodes.
+
+To make a set of barcodes and write this set to a file named `barcodes.txt`,
+use the following command:
+
+    barcode make barcodes.txt
+
+`barcodes.txt` will now contain a list of barcodes that all have length 8, and
+no barcode will contain a mononucleotide stretch longer than 2.
+
+The length of the barcodes can be controlled with the `-l` parameter, the
+minimum edit distance is controlled with the `-d` option and the maximum
+mononucleotide stretch length can be set with the `-s` option. So if we want to
+make a list of barcodes of length 10, a minimum edit distance of 5 (allowing
+for the correction of 2 read errors) and a maximum mononucleotide stretch of 1,
+we use the following command:
+
+    barcode make -d 5 -l 10 -s 1 barcodes.txt
+
+To verify a list of existing barcodes, use the command:
+
+    barcode test barcode.txt
+
+This will check the distance between any pair of barcodes and will tell you how
+many barcodes violate the distance constraint. Again, the minimum edit distance
+can be set with the `-d` parameter.
+
+Additionally, a good set of barcodes can be extracted by providing an output
+file via the `-o` option:
+
+    barcode test -o good_barcodes.txt barcodes.txt