Mercurial > repos > devteam > kraken_report
annotate README.rst @ 2:c4fb5dc47fce draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
| author | devteam |
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| date | Mon, 21 Mar 2016 12:05:59 -0400 |
| parents | f2757ab26483 |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 Introduction |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 ============ |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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3 |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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4 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is a taxonomic sequence |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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5 classifier that assigns taxonomic labels to short DNA reads. It does |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 this by examining the :math:`k`-mers within a read and querying a |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 database with those :math:`k`-mers. This database contains a mapping of |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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8 every :math:`k`-mer in |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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9 `Kraken <http://ccb.jhu.edu/software/kraken/>`__'s genomic library to |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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10 the lowest common ancestor (LCA) in a taxonomic tree of all genomes that |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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11 contain that :math:`k`-mer. The set of LCA taxa that correspond to the |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 :math:`k`-mers in a read are then analyzed to create a single taxonomic |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 label for the read; this label can be any of the nodes in the taxonomic |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 tree. `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is designed to be |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 rapid, sensitive, and highly precise. Our tests on various real and |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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16 simulated data have shown |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 slightly lower than Megablast with precision being slightly higher. On a |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 set of simulated 100 bp reads, |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 `Kraken <http://ccb.jhu.edu/software/kraken/>`__ processed over 1.3 |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 million reads per minute on a single core in normal operation, and over |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 4.1 million reads per minute in quick operation. |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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24 The latest released version of Kraken will be available at the `Kraken |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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25 website <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 to the Kraken source code are available at the `Kraken GitHub |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 repository <https://github.com/DerrickWood/kraken>`__. |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 research, please cite the `Kraken |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 paper <http://genomebiology.com/2014/15/3/R46>`__. Thank you! |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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32 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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33 System Requirements |
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34 =================== |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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35 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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36 Note: Users concerned about the disk or memory requirements should read |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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37 the paragraph about MiniKraken, below. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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38 |
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f2757ab26483
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 - **Disk space**: Construction of Kraken's standard database will |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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40 require at least 160 GB of disk space. Customized databases may |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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41 require more or less space. Disk space used is linearly proportional |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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42 to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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43 default database contains just under 6 billion (6e9) distinct |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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44 :math:`k`-mers. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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45 |
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46 In addition, the disk used to store the database should be |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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47 locally-attached storage. Storing the database on a network |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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48 filesystem (NFS) partition can cause Kraken's operation to be very |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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49 slow, or to be stopped completely. As NFS accesses are much slower |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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50 than local disk accesses, both preloading and database building will |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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51 be slowed by use of NFS. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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52 |
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53 - **Memory**: To run efficiently, Kraken requires enough free memory to |
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54 hold the database in RAM. While this can be accomplished using a |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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55 ramdisk, Kraken supplies a utility for loading the database into RAM |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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56 via the OS cache. The default database size is 75 GB (as of Feb. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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57 2015), and so you will need at least that much RAM if you want to |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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58 build or run with the default database. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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59 |
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60 - **Dependencies**: Kraken currently makes extensive use of Linux |
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61 utilities such as sed, find, and wget. Many scripts are written using |
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62 the Bash shell, and the main scripts are written using Perl. Core |
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63 programs needed to build the database and run the classifier are |
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64 written in C++, and need to be compiled using g++. Multithreading is |
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65 handled using OpenMP. Downloads of NCBI data are performed by wget |
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66 and in some cases, by rsync. Most Linux systems that have any sort of |
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67 development package installed will have all of the above listed |
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68 programs and libraries available. |
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69 |
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70 Finally, if you want to build your own database, you will need to |
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71 install the |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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72 `Jellyfish <http://www.cbcb.umd.edu/software/jellyfish/>`__ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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73 :math:`k`-mer counter. Note that Kraken only supports use of |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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74 Jellyfish version 1. Jellyfish version 2 is not yet compatible with |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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75 Kraken. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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76 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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77 - **Network connectivity**: Kraken's standard database build and |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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78 download commands expect unfettered FTP and rsync access to the NCBI |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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79 FTP server. If you're working behind a proxy, you may need to set |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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80 certain environment variables (such as ``ftp_proxy`` or |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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81 ``RSYNC_PROXY``) in order to get these commands to work properly. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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82 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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83 - **MiniKraken**: To allow users with low-memory computing environments |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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84 to use Kraken, we supply a reduced standard database that can be |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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85 downloaded from the Kraken web site. When Kraken is run with a |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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86 reduced database, we call it MiniKraken. |
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87 |
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88 The database we make available is only 4 GB in size, and should run |
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89 well on computers with as little as 8 GB of RAM. Disk space required |
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90 for this database is also only 4 GB. |
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91 |
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92 |