Map Reads with UGENE Genome Aligner Element

Unique UGENE algorithm for aligning short reads to a reference genome.

Element type: genome-aligner

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output file nameBase name of the output file. ‘out.sam’ by default.out.samoutnamestring
Reference genomePath to an indexed reference genome.referencestring
Is absolute mismatches values?Choose between absolute or percentage mismatches values mode.Trueif-absolute-mismatches-valueboolean
Absolute mismatchesNumber of mismatches allowed while aligning reads.0absolute-mismatchesnumeric
Align reverse complement readsSet this option to align both direct and reverse complement reads.Falsereverseboolean
Use “best”-modeReport only the best alignment for each read (in terms of mismatches).Truebestboolean
Omit reads with qualities lower thanOmit reads with qualities lower than the specified value. Set “0” to switch off this option.0quality-thresholdnumeric

Input/Output Ports

The element has 1 input port:

  • Name in GUI: Genome aligner 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: Genome aligner output data
  • Name in Workflow File: out-data

Slots:

Slot In GUISlot in Workflow FileType
Assembly URLassembly-outstring
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