Mercurial > repos > devteam > kraken_report
changeset 0:8bbf903bf0cb draft
Uploaded
| author | devteam |
|---|---|
| date | Wed, 22 Apr 2015 13:04:06 -0400 |
| parents | |
| children | bb3d55e8ef3d |
| files | README.md kraken-report.xml macros.xml tool-data/kraken_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 5 files changed, 181 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Apr 22 13:04:06 2015 -0400 @@ -0,0 +1,88 @@ +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-report.xml Wed Apr 22 13:04:06 2015 -0400 @@ -0,0 +1,50 @@ +<tool id="kraken-report" name="Kraken-report" version="1.0.0"> + <description> + View a sample report of your classification + </description> + <macros> + <import>macros.xml</import> + </macros> + <command> + <![CDATA[ + kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" + ]]> + </command> + <inputs> + <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" /> + <expand macro="input_database" /> + </inputs> + <outputs> + <data format="tabular" name="output_report" /> + </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.*** + + + +**The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:** + + 1)Percentage of reads covered by the clade rooted at this taxon + + 2)Number of reads covered by the clade rooted at this taxon + + 3)Number of reads assigned directly to this taxon + + 4)A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply -. + + 5)NCBI taxonomy ID + + 6)Indented scientific name + +The scientific names are indented using spaces, according to the tree +structure specified by the taxonomy. + ]]> + </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 13:04:06 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 && 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 13:04:06 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 13:04:06 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>