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Performs alignment of short reads with BWA.

Element type: align-reads-with-bwa


ParameterDescriptionDefault valueParameter in Workflow FileType
Output directory Directory to save BWA-MEM output files.
output-dir string
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
Use missing probUse missing prob instead maximum edit distance.Trueuse-miss-probboolean
Missing prob

Missing prob (-n).

Seed lengthSeed length (-l).32seed-lengthnumeric
Max gap opensMax gap opens (-o).1max-gapnumeric
Index algorithmIndex algorithm (-a).isindex-algstring
Best hits

Best hits (-R).

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

Enable long gaps.

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

Indel offset (-i).

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