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+Introduction
+============
+
+[Kraken] is a taxonomic sequence classifier that assigns taxonomic
+labels to short DNA reads. It does this by examining the $k$-mers
+within a read and querying a database with those $k$-mers. This database
+contains a mapping of every $k$-mer in [Kraken]'s genomic library to the
+lowest common ancestor (LCA) in a taxonomic tree of all genomes that
+contain that $k$-mer. The set of LCA taxa that correspond to the $k$-mers
+in a read are then analyzed to create a single taxonomic label for the
+read; this label can be any of the nodes in the taxonomic tree.
+[Kraken] is designed to be rapid, sensitive, and highly precise. Our
+tests on various real and simulated data have shown [Kraken] to have
+sensitivity slightly lower than Megablast with precision being slightly
+higher. On a set of simulated 100 bp reads, [Kraken] processed over 1.3
+million reads per minute on a single core in normal operation, and over
+4.1 million reads per minute in quick operation.
+
+The latest released version of Kraken will be available at the
+[Kraken website], and the latest updates to the Kraken source code
+are available at the [Kraken GitHub repository].
+
+If you use [Kraken] in your research, please cite the [Kraken paper].
+Thank you!
+
+[Kraken]:                     http://ccb.jhu.edu/software/kraken/
+[Kraken website]:             http://ccb.jhu.edu/software/kraken/
+[Kraken paper]:               http://genomebiology.com/2014/15/3/R46
+[Kraken GitHub repository]:   https://github.com/DerrickWood/kraken
+
+
+System Requirements
+===================
+
+Note: Users concerned about the disk or memory requirements should
+read the paragraph about MiniKraken, below.
+
+* **Disk space**: Construction of Kraken's standard database will require at
+    least 160 GB of disk space. Customized databases may require
+    more or less space.  Disk space used is linearly proportional
+    to the number of distinct $k$-mers; as of Feb. 2015, Kraken's
+    default database contains just under 6 billion (6e9) distinct $k$-mers.
+
+    In addition, the disk used to store the database should be
+    locally-attached storage. Storing the database on a network
+    filesystem (NFS) partition can cause Kraken's operation to be
+    very slow, or to be stopped completely. As NFS accesses are
+    much slower than local disk accesses, both preloading and database
+    building will be slowed by use of NFS.
+
+* **Memory**: To run efficiently, Kraken requires enough free memory to
+    hold the database in RAM. While this can be accomplished using a
+    ramdisk, Kraken supplies a utility for loading the database into
+    RAM via the OS cache. The default database size is 75 GB (as of
+    Feb. 2015), and so you will need at least that much RAM if you want
+    to build or run with the default database.
+
+* **Dependencies**: Kraken currently makes extensive use of Linux utilities
+    such as sed, find, and wget. Many scripts are written using the
+    Bash shell, and the main scripts are written using Perl. Core
+    programs needed to build the database and run the classifier are
+    written in C++, and need to be compiled using g++.  Multithreading
+    is handled using OpenMP.  Downloads of NCBI data are performed by
+    wget and in some cases, by rsync.  Most Linux systems that have any
+    sort of development package installed will have all of the above
+    listed programs and libraries available.
+
+    Finally, if you want to build your own database, you will need to
+    install the [Jellyfish] $k$-mer counter.  Note that Kraken only
+    supports use of Jellyfish version 1.  Jellyfish version 2 is not
+    yet compatible with Kraken.
+
+* **Network connectivity**: Kraken's standard database build and download
+    commands expect unfettered FTP and rsync access to the NCBI FTP
+    server. If you're working behind a proxy, you may need to set
+    certain environment variables (such as `ftp_proxy` or `RSYNC_PROXY`)
+    in order to get these commands to work properly.
+
+* **MiniKraken**: To allow users with low-memory computing environments to
+    use Kraken, we supply a reduced standard database that can be
+    downloaded from the Kraken web site. When Kraken is run with a
+    reduced database, we call it MiniKraken.
+
+    The database we make available is only 4 GB in size, and should
+    run well on computers with as little as 8 GB of RAM. Disk space
+    required for this database is also only 4 GB.
+
+[Jellyfish]:  http://www.cbcb.umd.edu/software/jellyfish/
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