Build a CLARK database from a set of reference sequences ("targets"). NCBI taxonomy data are used to map the accession number found in each reference sequence to its taxonomy ID.
Element type: clark-build
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Database | A folder that should be used to store the database files. | database | string | |
| Genomic library | Genomes that should be used to build the database ("targets"). The genomes should be specified in FASTA format. There should be one FASTA file per reference sequence. A sequence header must contain an accession number (i.e., >accession.number ... or >gi|number|ref|accession.number| ...). | taxonomy | url-datasets | |
| Taxonomy rank | Set the taxonomy rank for the database. CLARK classifies metagenomic samples by using only one taxonomy rank. So as a general rule, consider first the genus or species rank, then if a high proportion of reads cannot be classified, reset your targets definition at a higher taxonomy rank (e.g., family or phylum). | Species | taxonomy-rank | number |
Input/Output Ports
The element has 1 output port:
Name in GUI: Output CLARK database
Name in Workflow File: out
Slots:
| SlotInGUI | Slot in Workflow File | Type |
|---|---|---|
| Output URL | url | string |