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1 Introduction
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2 ============
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3
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4 [Kraken] is a taxonomic sequence classifier that assigns taxonomic
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5 labels to short DNA reads. It does this by examining the $k$-mers
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6 within a read and querying a database with those $k$-mers. This database
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7 contains a mapping of every $k$-mer in [Kraken]'s genomic library to the
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8 lowest common ancestor (LCA) in a taxonomic tree of all genomes that
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9 contain that $k$-mer. The set of LCA taxa that correspond to the $k$-mers
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10 in a read are then analyzed to create a single taxonomic label for the
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11 read; this label can be any of the nodes in the taxonomic tree.
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12 [Kraken] is designed to be rapid, sensitive, and highly precise. Our
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13 tests on various real and simulated data have shown [Kraken] to have
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14 sensitivity slightly lower than Megablast with precision being slightly
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15 higher. On a set of simulated 100 bp reads, [Kraken] processed over 1.3
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16 million reads per minute on a single core in normal operation, and over
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17 4.1 million reads per minute in quick operation.
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18
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19 The latest released version of Kraken will be available at the
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20 [Kraken website], and the latest updates to the Kraken source code
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21 are available at the [Kraken GitHub repository].
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22
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23 If you use [Kraken] in your research, please cite the [Kraken paper].
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24 Thank you!
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25
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26 [Kraken]: http://ccb.jhu.edu/software/kraken/
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27 [Kraken website]: http://ccb.jhu.edu/software/kraken/
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28 [Kraken paper]: http://genomebiology.com/2014/15/3/R46
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29 [Kraken GitHub repository]: https://github.com/DerrickWood/kraken
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30
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31
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32 System Requirements
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33 ===================
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34
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35 Note: Users concerned about the disk or memory requirements should
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36 read the paragraph about MiniKraken, below.
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37
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38 * **Disk space**: Construction of Kraken's standard database will require at
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39 least 160 GB of disk space. Customized databases may require
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40 more or less space. Disk space used is linearly proportional
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41 to the number of distinct $k$-mers; as of Feb. 2015, Kraken's
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42 default database contains just under 6 billion (6e9) distinct $k$-mers.
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43
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44 In addition, the disk used to store the database should be
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45 locally-attached storage. Storing the database on a network
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46 filesystem (NFS) partition can cause Kraken's operation to be
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47 very slow, or to be stopped completely. As NFS accesses are
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48 much slower than local disk accesses, both preloading and database
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49 building will be slowed by use of NFS.
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50
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51 * **Memory**: To run efficiently, Kraken requires enough free memory to
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52 hold the database in RAM. While this can be accomplished using a
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53 ramdisk, Kraken supplies a utility for loading the database into
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54 RAM via the OS cache. The default database size is 75 GB (as of
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55 Feb. 2015), and so you will need at least that much RAM if you want
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56 to build or run with the default database.
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57
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58 * **Dependencies**: Kraken currently makes extensive use of Linux utilities
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59 such as sed, find, and wget. Many scripts are written using the
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60 Bash shell, and the main scripts are written using Perl. Core
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61 programs needed to build the database and run the classifier are
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62 written in C++, and need to be compiled using g++. Multithreading
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63 is handled using OpenMP. Downloads of NCBI data are performed by
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64 wget and in some cases, by rsync. Most Linux systems that have any
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65 sort of development package installed will have all of the above
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66 listed programs and libraries available.
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67
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68 Finally, if you want to build your own database, you will need to
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69 install the [Jellyfish] $k$-mer counter. Note that Kraken only
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70 supports use of Jellyfish version 1. Jellyfish version 2 is not
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71 yet compatible with Kraken.
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72
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73 * **Network connectivity**: Kraken's standard database build and download
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74 commands expect unfettered FTP and rsync access to the NCBI FTP
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75 server. If you're working behind a proxy, you may need to set
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76 certain environment variables (such as `ftp_proxy` or `RSYNC_PROXY`)
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77 in order to get these commands to work properly.
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78
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79 * **MiniKraken**: To allow users with low-memory computing environments to
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80 use Kraken, we supply a reduced standard database that can be
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81 downloaded from the Kraken web site. When Kraken is run with a
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82 reduced database, we call it MiniKraken.
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83
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84 The database we make available is only 4 GB in size, and should
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85 run well on computers with as little as 8 GB of RAM. Disk space
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86 required for this database is also only 4 GB.
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87
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88 [Jellyfish]: http://www.cbcb.umd.edu/software/jellyfish/ |
