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Performs alignment of short reads with BWA-MEM.

Element type: bwamem-id


ParameterDescriptionDefault valueParameter in Workflow FileType
Output directory Directory to save BWA-MEM output files.


Reference genomePath to an indexed reference genome.
Output file nameBase name of the output file. 'out.sam' by default.out.samoutnamestring
LibraryIs this library mate-paired?single-endlibrarystring
Number of threadsNumber of threads (-t).1threadsnumeric
Min seed length

Path to an indexed reference genome (-k).

Index algorithm

Index algorithm (-a).

Band widthBandwidth for banded alignment (-w).100band-widthnumeric
DropoffOff-diagonal X-dropoff (-d).100dropoffnumeric
Internal seed lengthLook for internal seeds inside a seed longer than {-k} (-r).1.50000seed-lookupnumeric
Skip seed threshold

Skip seeds with more than INT occurrences (-c).

Drop chain thresholdDrop chains shorter than FLOAT fraction of the longest overlapping chain (-D).0.5drop-chainsnumeric
Rounds of made rescuesPerform at most INT rounds of mate rescues for each read (-m).100mate-rescuenumeric
Skip mate rescue

Skip mate rescue (-S).

Skip pairingSkip pairing; mate rescue performed unless -S also in use (-P).Falseskip-pairingboolean
Matching score

Score for a sequence match (-A).

Mismatch penaltyPenalty for a mismatch (-B).4mistmatch-penaltynumeric
Gap open penaltyGap open penalty (-O).6gap-open-penaltynumeric
Gap extension penaltyGap extension penalty; a gap of size k cost {-O} (-E).1gap-ext-penaltynumeric
Penalty for clippingPenalty for clipping (-L).5clipping-penaltynumeric
Penalty unpairedPenalty for an unpaired read pair (-U).17inpaired-panaltynumeric
Score thresholdMinimum score to output (-T).30 score-thresholdnumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: BWA data

Name in Workflow File: in-data


Slot In GUISlot in Workflow FileType
URL of a file with mate readsreadsurlstring
URL of a file with readsreadspairedurlstring

And 1 output port:

Name in GUI: BWA-MEM output data

Name in Workflow File: out-data


Slot In GUISlot in Workflow FileType
Assembly URLassembly-outstring
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