Performs alignment of short reads with BWA-MEM.
Element type: bwamem-id
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 |
| Number of threads | Number of threads (-t). | 1 | threads | numeric |
| Min seed length | Path to an indexed reference genome (-k). | 19 | min-seed | numeric |
| Index algorithm | Index algorithm (-a). | autodetect | index-alg | string |
| Band width | Bandwidth for banded alignment (-w). | 100 | band-width | numeric |
| Dropoff | Off-diagonal X-dropoff (-d). | 100 | dropoff | numeric |
| Internal seed length | Look for internal seeds inside a seed longer than {-k} (-r). | 1.50000 | seed-lookup | numeric |
| Skip seed threshold | Skip seeds with more than INT occurrences (-c). | 10000 | seed-threshold | numeric |
| Drop chain threshold | Drop chains shorter than FLOAT fraction of the longest overlapping chain (-D). | 0.5 | drop-chains | numeric |
| Rounds of made rescues | Perform at most INT rounds of mate rescues for each read (-m). | 100 | mate-rescue | numeric |
| Skip mate rescue | Skip mate rescue (-S). | False | skip-mate-rescues | boolean |
| Skip pairing | Skip pairing; mate rescue performed unless -S also in use (-P). | False | skip-pairing | boolean |
| Matching score | Score for a sequence match (-A). | 1 | match-score | numeric |
| Mismatch penalty | Penalty for a mismatch (-B). | 4 | mistmatch-penalty | numeric |
| Gap open penalty | Gap open penalty (-O). | 6 | gap-open-penalty | numeric |
| Gap extension penalty | Gap extension penalty; a gap of size k cost {-O} (-E). | 1 | gap-ext-penalty | numeric |
| Penalty for clipping | Penalty for clipping (-L). | 5 | clipping-penalty | numeric |
| Penalty unpaired | Penalty for an unpaired read pair (-U). | 17 | inpaired-panalty | numeric |
| Score threshold | Minimum score to output (-T). | 30 | score-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-MEM output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Assembly URL | assembly-out | string |