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changeset 0:60d9479c58d6 draft

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author devteam
date Wed, 22 Apr 2015 13:03:54 -0400
parents
children f093ba52debe
files README.md kraken-filter.xml macros.xml tool-data/kraken_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 5 files changed, 175 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Apr 22 13:03:54 2015 -0400
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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/
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-filter.xml	Wed Apr 22 13:03:54 2015 -0400
@@ -0,0 +1,44 @@
+<tool id="kraken-filter" name="Filter Kraken" version="1.0.0">
+    <description>
+        by confidence score
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+        <![CDATA[
+        kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output"
+        ]]>
+    </command>
+    <inputs>
+        <param format="tabular" label="Kraken classified output" name="input" type="data" />
+        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" />
+        <expand macro="input_database" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="filtered_output" />
+    </outputs>
+    <help>
+<![CDATA[
+
+***Note that the database used must be the same as the one used to generate
+the output file, or the report script may encounter problems.***
+
+A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output given earlier:
+
+"562:13 561:4 A:31 0:1 562:3" would indicate that:
+
+    the first 13 k-mers mapped to taxonomy ID #562
+    the next 4 k-mers mapped to taxonomy ID #561
+    the next 31 k-mers contained an ambiguous nucleotide
+    the next k-mer was not in the database
+    the last 3 k-mers mapped to taxonomy ID #562
+
+In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
+    ]]>
+    </help>
+    <expand macro="version_command" />
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Apr 22 13:03:54 2015 -0400
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.10.5">kraken</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code description="Tool exception" level="fatal" range="1:" />
+        </stdio>
+    </xml>
+    <xml name="version_command">
+        <version_command>export LC_ALL=C &amp;&amp; kraken --version</version_command>
+    </xml>
+    <xml name="input_database">
+        <param label="Select a Kraken database" name="kraken_database" type="select">
+            <options from_data_table="kraken_databases">
+                <validator message="No databases are available built-in" type="no_options" />
+            </options>
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
+        </citations>
+    </xml>
+    <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.path}/${kraken_database.fields.name}</token>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Apr 22 13:03:54 2015 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Kraken database in the required format -->
+    <table name="kraken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/kraken_databases.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Apr 22 13:03:54 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="kraken" version="0.10.5">
+      <repository changeset_revision="c949a8bd92ec" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>