Update README to include publication info

README.md

@@ -1,10 +1,19 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/kraken2/README.html)
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-kraken2
-=======
+Kraken 2
+========
 
 The second version of the Kraken taxonomic sequence classification system
 
-Please refer to the Operating Manual (in docs/MANUAL.html) for details on
+Please refer to the Operating Manual (in `docs/MANUAL.html`) for details on
 how to use Kraken 2.
+
+Publications
+------------
+
+For additional implementation details and guidance on using Kraken 2, you can also refer to:
+- The [paper describing the first version of Kraken](https://dx.doi.org/10.1186/gb-2014-15-3-r46).  Note that Kraken 2 is a rewrite of Kraken 1 and is not backwards compatible with Kraken 1.
+- The [paper describing KrakenUniq](https://dx.doi.org/10.1186/s13059-018-1568-0).  KrakenUniq's HLL-based functionality is incorporated in Kraken 2 when using the `--report-minimizer-data` flag described in the Operating Manual.
+- The [Kraken 2 paper](https://dx.doi.org/10.1186/s13059-019-1891-0).
+- A [protocol paper describing use of Kraken 2](https://dx.doi.org/10.1038/s41596-022-00738-y).