# HG changeset patch # User devteam # Date 1429722204 14400 # Node ID 7d6b55e6417ed1aec1127890d1db445e2ce61145 Uploaded diff -r 000000000000 -r 7d6b55e6417e README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Apr 22 13:03:24 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 diff -r 000000000000 -r 7d6b55e6417e kraken.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kraken.xml Wed Apr 22 13:03:24 2015 -0400 @@ -0,0 +1,94 @@ + + + + assign taxonomic labels to short DNA reads + + + macros.xml + + + "${translated}" + ]]> + + + + + + + + + (split_reads) + + + (split_reads) + + + (draw_histogram) + + + + + + sequences.kraken + + or + + kraken --db $DBNAME sequences.fq > sequences.kraken + + + -DBNAME is the name of the Kraken Database to be used. + + -sequences.fa or sequences.fq is the FASTA or FASTQ input file containing the desired sequences for classification. + + -sequences.kraken is the generated output. + + + + **Options** + + The kraken program allows several different sequencing modifiers (parameters): + + **Multithreading:** Use the --threads NUM switch to use multiple threads. + + **Sequence filtering:** Classified or unclassified sequences can be sent to a file for later processing, using the --classified-out and --unclassified-out switches, respectively. + + + + **Output Format** + + Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are: + + 1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified. + 2. The sequence ID, obtained from the FASTA/FASTQ header. + 3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified. + 4. The length of the sequence in bp. + + 5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that: + a) the first 13 k-mers mapped to taxonomy ID #562 + b) the next 4 k-mers mapped to taxonomy ID #561 + c) the next 31 k-mers contained an ambiguous nucleotide + d) the next k-mer was not in the database + e) the last 3 k-mers mapped to taxonomy ID #562 + ]]> + + + + + + \ No newline at end of file diff -r 000000000000 -r 7d6b55e6417e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 22 13:03:24 2015 -0400 @@ -0,0 +1,29 @@ + + + + + kraken + + + + + + + + + export LC_ALL=C && kraken --version + + + + + + + + + + + 10.1186/gb-2014-15-3-r46 + + + --db ${kraken_database.fields.path}/${kraken_database.fields.name} + \ No newline at end of file diff -r 000000000000 -r 7d6b55e6417e tool-data/kraken_databases.loc.sample diff -r 000000000000 -r 7d6b55e6417e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 22 13:03:24 2015 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+ diff -r 000000000000 -r 7d6b55e6417e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 22 13:03:24 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +