Build a Kraken database from a genomic library or shrink a Kraken database.
Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Mode | Select "Build" to create a new database from a genomic library (--build). | Build |
Database | Name of the output Kraken database (corresponds to --db that is used with --build, and to --new-db that is used with --shrink). | |
Genomic library | Genomes that should be used to build the database. | |
K-mer length | K-mer length in bp (--kmer-len). | 31 |
Minimizer length | Minimizer length in bp (--minimizer-len). The minimizers serve to keep k-mers that are adjacent in query sequences close to each other in the database, which allows Kraken to exploit the CPU cache. | 15 |
Maximum database size | By default, a full database build is done. To shrink the database before the full build, input the size of the database in Mb (this corresponds to the --max-db-size parameter, but Mb is used instead of Gb). The size is specified together for the database and the index. | No limit |
Clean | Remove unneeded files from a built database to reduce the disk usage (--clean). | True |
Work on disk | Performs most operations on disk rather than in RAM (this will slow down build in most cases). | False |
Jellyfiah hash size | The "kraken-build" tool uses the "jellyfish" tool. This parameter specifies the hash size for Jellyfish. Supply a smaller hash size to Jellyfish, if you encounter problems with allocating enough memory during the build process (--jellyfish-hash-size). | Skip |
Number of threads | Use multiple threads (--threads). | 8 |
Parameters in Workflow File
Type: kraken-build
Parameter | Parameter in the GUI | Type |
---|---|---|
mode | Mode | string |
database | Database | string |
genomic-library | Genomic library | url-datasets |
k-mer-length | K-mer length | number |
minimizer-length | Minimizer length | number |
maximum-database-size | Maximum database size | number |
clean | Clean | bool |
work-on-disk | Work on disk | bool |
jellyfish-hash-size | Jellyfiah hash size | number |
threads | Number of threads | number |
Input/Output Ports
The element has 1 output port:
Name in GUI: Output Kraken database
Name in Workflow File: out
Slots:
SlotInGUI | Slot in Workflow File | Type |
---|---|---|
Output URL | url | string |