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  • Align reads with BWA-MEM

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Performs alignment of short reads with BWA-MEM.

Parameters in GUI


ParameterDescriptionDefault value
Output directory Directory to save BWA MEM output files. 
Reference genomePath to indexed reference genome. 
Output file nameBase name of the output file. 'out.sam' by default.out.sam
Number of threadsNumber of threads (-t).1
Min seed length

Path to indexed reference genome (-k).

Band widthBand width for banded alignment (-w).100
DropoffOff-diagonal X-dropoff (-d).100
Internal seed lengthLook for internal seeds inside a seed longer than {-k} (-r).1.50000
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).0.5
Rounds of made rescuesPerform at most INT rounds of mate rescues for each read (-m).100
Skip mate rescue

Skip mate rescue (-S).

Skip pairingSkip pairing; mate rescue performed unless -S also in use (-P).False
Mismatch penalty

Score for a sequence match (-A).

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

Parameters in Workflow File