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Unique UGENE algorithm for aligning short reads to reference genome.

Parameters in GUI

 

ParameterDescriptionDefault value
Output file name Base name of the output file. 'out.sam' by default.out.sam
Reference genomePath to indexed reference genome. 
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.

True
Absolute mismatchesNumber of mismatches allowed while aligning reads.0
Align reverse complement reads

Set this option to align both direct and reverse complement reads.

False
Use "best"-modeReport only the best alignment for each read (in terms of mismatches).True
Omit reads with qualities lower than

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

Set "0" to switch off this option.

0

Parameters in Workflow File

Type: genome-aligner

ParameterParameter in the GUIType
outnameOutput file name string
referenceReference genomestring 
if-absolute-mismatches-valueIs absolute mismatches values?boolean
absolute-mismatchesAbsolute mismatchesnumeric
reverseAlign reverse complement readsboolean
bestUse "best"-modeboolean
quality-thresholdOmit reads with qualities lower thannumeric

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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