Unique UGENE algorithm for aligning short reads to reference genome.
Element type: genome-aligner
Parameters
Parameter | Description | Default value | Parameter in Workflow File | Type |
---|---|---|---|---|
Output file name | Base name of the output file. 'out.sam' by default. | out.sam | outname | string |
Reference genome | Path to an indexed reference genome. | reference | string | |
Is absolute mismatches values? | true - absolute mismatches mode is used false - percentage mismatches mode is used You can choose absolute or percentage mismatches values mode. | True | if-absolute-mismatches-value | boolean |
Absolute mismatches | Number of mismatches allowed while aligning reads. | 0 | absolute-mismatches | numeric |
Align reverse complement reads | Set this option to align both direct and reverse complement reads. | False | reverse | boolean |
Use "best"-mode | Report only the best alignment for each read (in terms of mismatches). | True | best | boolean |
Omit reads with qualities lower than | Omit reads with qualities lower than the specified value. Reads that have no qualities are not omitted. Set "0" to switch off this option. | 0 | quality-threshold | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Genome aligner data
Name in Workflow File: in-data
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
URL of a file with mate reads | readsurl | string |
URL of a file with reads | readspairedurl | string |
And 1 output port:
Name in GUI: Genome aligner output data
Name in Workflow File: out-data
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Assembly URL | assembly-out | string |