Unique UGENE algorithm for aligning short reads to reference genome.
Parameters in GUI
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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 |
Type: genome-aligner
| 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 |