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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

Type: bwamem-id

ParameterParameter in the GUIType
output-dirOutput directory


referenceReference genomestring
outnameOutput file namestring
threadsNumber of threadsnumeric
min-seedMin seed lengthnumeric
band-widthBand widthnumeric
seed-lookupInternal seed lengthnumeric
seed-thresholdSkip seed thresholdnumeric
drop-chainsDrop chain thresholdnumeric
mate-rescueRounds of made rescuesnumeric
skip-mate-rescuesSkip mate rescueboolean
skip-pairingSkip pairingboolean
match-scoreMismatch penaltynumeric
mistmatch-penaltyMismatch penaltynumeric
gap-open-penaltyGap open penaltynumeric
gap-ext-penaltyGap extension penaltynumeric
clipping-penaltyPenalty for clippingnumeric
inpaired-panaltyPenalty unpairednumeric
 score-thresholdScore 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