Description
It is a customized version of UGENE 1.12 with additional algorithms for forensics research.
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How to use
Find intersections
ugenecl --task=intersections <parameters>
The list of parameters
- sample – Sample file path.
- markers-dir – Markers directory path.
- acc – Comparing accuracy.
- report – Output report file path.
- sample-reports-dir – Path to the output directory with sequence lists. Default: sample_reports.
- sep – CSV report separator. Default: ;.
Example
ugenecl --task=intersections --sample=D:/sample1.fasta --markers-dir=D:/markers/ --report=D:/report.txt --acc=98
Sequence dereplication
ugenecl --task=dereplicate <parameters>
The list of parameters
- in – Sample file path.
- out – Output (dreplicated) file path.
- accuracy – Comparing accuracy.
- report – Output report file path.
Example
ugenecl --task=dereplicate --in=D:/18_345.fasta --out=D:/out.fa --accuracy=95 --report=D:/report.txt
Reduce sequences
ugenecl --task=reduce <parameters>
The list of parameters
- in-seqs – Path to a sample file to reduce.
- in-db – Path to a small database file of sequence.
- accuracy – Comparing accuracy.
- out – Output reduced file path.
Example
ugenecl --task=reduce --in-seqs=D:/18_345.fasta --in-db=D:/small-db.fasta --out=D:/reduced.fasta --accuracy=99.0
Alignment distance
The list of parameters
ugenecl --task=distance <parameters>
- in-msa – Input alignment file path.
- in-seqs – Input sample file path.
- out – Output report file path.
- sep – CSV report separator. Default: ;.
Example
ugenecl --task=distance --in-msa=D:/S6.aln --in-seqs=D:/S6.fasta --out=D:/report.txt --sep=","