Unique UGENE algorithm for aligning short reads to reference genome.

Element type: genome-aligner

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output file name Base name of the output file. 'out.sam' by default.out.samoutname string
Reference genomePath to an indexed reference genome.
referencestring 
Is absolute mismatches values?

true - absolute mismatches mode is used

false - percentage mismatches mode is used

You can choose absolute or percentage mismatches values mode.

Trueif-absolute-mismatches-valueboolean
Absolute mismatchesNumber of mismatches allowed while aligning reads.0absolute-mismatchesnumeric
Align reverse complement reads

Set 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 than

Omit reads with qualities lower than the specified value. Reads that have no qualities are not omitted.

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