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Performs alignment of short reads with BWA.

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
Use missing probUse missing prob instead maximum edit distance.True
Missing prob

Missing prob (-n).

Seed lengthSeed length (-l).32
Max gap opensMax gap opens (-o).1
Index algorithmIndex algorithm (-a).is
Best hits

Best hits (-R).

Long-scaled gap penalty for long deletionsLong-scaled gap penalty for long deletions (-L).False
Non iterative modeNon iterative mode (-N).False
Enable long gaps

Enable long gaps.

Max gap extensionsMax gap extensions (-e).0
Indel offset

Indel offset (-i).

Max long deletions extensionsMax long deletions extensions(-d).10
Barcode lengthBarcode length (-B).0
Max queue entriesMax queue entries (-m).2000000
ThreadsThreads (-t).4
Max seed differenciesMax seed differencies (-k).2
Mismatch penaltyMismatch penalty (-M).3
Gap open penaltyGap open penalty (-O).11
Gap extension penaltyGap extension penalty; a gap of size k cost (-E).4
Quality thresholdQuolity threshold (-q).0

Parameters in Workflow File

Type: align-reads-with-bwa

ParameterParameter in the GUIType
output-dirOutput directory  string
referenceReference genomestring 
outnameOutput file namestring
use-miss-probUse missing probboolean
missing-probMissing probnumeric
seed-lengthSeed lengthnumeric
max-gapMax gap opensnumeric
index-algIndex algorithmstring
best-hitsBest hitsnumeric
scaled-gapLong-scaled gap penalty for long deletionsboolean
non-iterativeNon iterative modeboolean
enable-long-gapsEnable long gapsboolean
gap-extensionsMax gap extensionsnumeric
indel-offsetIndel offsetnumeric
long-deletionsMax long deletions extensionsnumeric
barcode-lengthBarcode lengthnumeric
max-queueMax queue entriesnumeric
max-seedMax seed differenciesnumeric
mistmatch-penaltyMismatch penaltynumeric
gap-open-penaltyGap open penaltynumeric
gap-ext-penaltyGap extension penaltynumeric
quality-thresholdQuality 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 output data

Name in Workflow File: out-data


Slot In GUISlot in Workflow FileType
Assembly URLassembly-outstring
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