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