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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
LibraryIs this library mate-paired?single-end
Number of threadsNumber of threads (-t).1
Min seed length

Path to indexed reference genome (-k).

Index algorithm

Index algorithm (-a).

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
Matching score

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
index-algIndex algorithmstring
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-scoreMatching scorenumeric
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
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