Child pages
  • Align Reads with BWA Element
Skip to end of metadata
Go to start of metadata

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

Missing prob (-n).

0.04
Seed lengthSeed length (-l).32
Max gap opensMax gap opens (-o).1
Index algorithmIndex algorithm (-a).is
Best hits

Best hits (-R).

30
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.

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

Indel offset (-i).

5
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
num-threadsThreadsnumeric
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

Slots:

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

Slots:

Slot In GUISlot in Workflow FileType
Assembly URLassembly-outstring
  • No labels