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ugene --session-db=D:/session.ugenedb

--version

Shows version information.

--tmp-dir=<path_to_file>

Path to teporary folder.

--ini-file=<path_to_file>

Loads configuration from the specified .ini file. By default the UGENE.ini file is used.

--genome-aligner

UGENE Genome Aligner is an efficient and fast tool for short read alignment. It has 2 work modes: build index and align short reads (default mode).
If there is no index available for reference sequence it will be built on the fly.

Usage: ugene --genome-aligner { --option[=argument] }

The following options are available:
 

--build-index Use this flag to only build index for reference sequence.

--reference Path to reference genome sequence

--short-reads Path to short-reads data in FASTA or FASTQ format

--index Path to prebuilt index (base file name or with .idx extension). If not set, index is searched in system temporary directory. If --build-index option is applied, index will be saved to specified
path.

--result Path to output alignment in UGENEDB or SAM format (see --sam)

--memsize Memory size (in Mbs) reserved for short-reads. The bigger value the faster algorithm works. Default value depends on available system memory.

--ref-size Index fragmentation size (in Mbs). Small fragments better fit into RAM, allowing to load more short reads. Default value is 10.

--n-mis Absolute amount of allowed mismatches per every short-read (mutually exclusive with --pt-mis). Default value is 0.

--pt-mis Percentage amount of allowed mismatches per every short-read (mutually exclusive with --n-mis). Default value is 0.

--rev-comp Use both the read and its reverse complement during the aligning.

--best Report only about best alignments (in terms of mismatches).

--omit-size Omit reads with qualities lower than the specified value. Reads which have no qualities are not omitted. Default value is 0.

--sam Output aligned reads in SAM format. Default value is false.

For example:

Build index for reference sequence:
ugene --genome-aligner --build-index --reference=/path/to/ref


Align short reads using existing index:
ugene --genome-aligner --reference=/path/to/ref --short-reads=/path/to/reads --result=/path/to/result