Performs alignment of short reads with BWA.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save BWA-MEM output files. | |
| Reference genome | Path to an indexed reference genome. | |
| Output file name | Base name of the output file. 'out.sam' by default. | out.sam |
| Library | Is this library mate-paired? | single-end |
| Use missing prob | Use missing prob instead maximum edit distance. | True |
| Missing prob | Missing prob (-n). | 0.04 |
| Seed length | Seed length (-l). | 32 |
| Max gap opens | Max gap opens (-o). | 1 |
| Index algorithm | Index algorithm (-a). | is |
| Best hits | Best hits (-R). | 30 |
| Long-scaled gap penalty for long deletions | Long-scaled gap penalty for long deletions (-L). | False |
| Non iterative mode | Non iterative mode (-N). | False |
| Enable long gaps | Enable long gaps. | True |
| Max gap extensions | Max gap extensions (-e). | 0 |
| Indel offset | Indel offset (-i). | 5 |
| Max long deletions extensions | Max long deletions extensions(-d). | 10 |
| Barcode length | Barcode length (-B). | 0 |
| Max queue entries | Max queue entries (-m). | 2000000 |
| Threads | Threads (-t). | 4 |
| Max seed differencies | Max seed differencies (-k). | 2 |
| Mismatch penalty | Mismatch penalty (-M). | 3 |
| Gap open penalty | Gap open penalty (-O). | 11 |
| Gap extension penalty | Gap extension penalty; a gap of size k cost (-E). | 4 |
| Quality threshold | Quolity threshold (-q). | 0 |
Parameters in Workflow File
Type: align-reads-with-bwa
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| output-dir | Output directory | string |
| reference | Reference genome | string |
| outname | Output file name | string |
| library | Library | string |
| use-miss-prob | Use missing prob | boolean |
| missing-prob | Missing prob | numeric |
| seed-length | Seed length | numeric |
| max-gap | Max gap opens | numeric |
| index-alg | Index algorithm | string |
| best-hits | Best hits | numeric |
| scaled-gap | Long-scaled gap penalty for long deletions | boolean |
| non-iterative | Non iterative mode | boolean |
| enable-long-gaps | Enable long gaps | boolean |
| gap-extensions | Max gap extensions | numeric |
| indel-offset | Indel offset | numeric |
| long-deletions | Max long deletions extensions | numeric |
| barcode-length | Barcode length | numeric |
| max-queue | Max queue entries | numeric |
| num-threads | Threads | numeric |
| max-seed | Max seed differencies | numeric |
| mistmatch-penalty | Mismatch penalty | numeric |
| gap-open-penalty | Gap open penalty | numeric |
| gap-ext-penalty | Gap extension penalty | numeric |
| quality-threshold | Quality threshold | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: BWA 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: BWA output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Assembly URL | assembly-out | string |