BuildSuffixArraySettingsReference fragmentationReference fragmentation<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">This parameter influences the number of parts the
reference will be divided. It is better to make it bigger, but it influences the
amount of memory used during the alignment.</span></p></body></html><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">This parameter influences the number of parts the
reference will be divided. It is better to make it bigger, but it influences the
amount of memory used during the alignment.</span></p></body></html>ResourcesTotal memory usage:Total memory usage:System memory size:System memory size:GenomeAlignerSettingsFormFormChech this box if mismatches between the reference sequence and the reads are allowed.Check this box if mismatches between the reference sequence and the reads are allowed.Mismatches allowedMismatches allowedSelect the number of mismatched nucleotides allowed.Select the number of mismatched nucleotides allowed.Select the percentage of mismatches allowed. Note, that absolute number of mismatches can vary for different reads.Select the percentage of mismatches allowed. Note, that absolute number of mismatches can vary for different reads.Mismatches numberMismatches numberCommon parametersCommon parametersPercentage of mismatchesPercentage of mismatchesSet short reads aligning options.Set short reads aligning options.Use both the read and its reverse complement during aligning.Use both the read and its reverse complement during aligning.Align reverse complement readsAlign reverse complement reads<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">Report only about best alignments (in terms of mismatches).</span></p></body></html><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">Report only about best alignments (in terms of mismatches).</span></p></body></html>Use "best"-mode during the alignmentUse "best"-mode during the alignmentUse an openCL-enabled GPU during the aligning.Use an openCL-enabled GPU during the aligning.Use GPU-optimizationUse GPU-optimizationAdvanced parametersAdvanced parametersMaximum memory for short readsMaximum memory for short readsTotal memory usage:Total memory usage:System memory size:System memory size:Index parametersIndex parametersReference fragmentationReference fragmentationIndex memory usage size:Index memory usage size:You can choose a temporary directory for saving index files for the reference that will be built during the alignment. If you need to run this algorithm one more time with the same reference and with the same reference fragmentation parameter, you can use this prebuilt index that will be located in the temporary directory.Directory for index files:Folder for index files:Folder for index files:Omit reads with qualities lower than the specified value. Reads that have no qualities are not omited.Omit reads with qualities lower than the specified value. Reads that have no qualities are not omited.<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">Allows one to decrease the load on the computer on one side and to increase the computation speed of the task on the other side.
</span></p></body></html><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">Allows one to decrease the load on the computer on one side and to increase the computation speed of the task on the other side.
</span></p></body></html><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">This parameter influences the number of parts the
reference will be divided. It is better to make it bigger, but it influences the
amount of memory used during the alignment.</span></p></body></html><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">This parameter influences the number of parts the
reference will be divided. It is better to make it bigger, but it influences the
amount of memory used during the alignment.</span></p></body></html>You can choose a temporary folder for saving index files for the reference that will be built during the alignment. If you need to run this algorithm one more time with the same reference and with the same reference fragmentation parameter, you can use this prebuilt index that will be located in the temporary folder.You can choose a temporary folder for saving index files for the reference that will be built during the alignment. If you need to run this algorithm one more time with the same reference and with the same reference fragmentation parameter, you can use this prebuilt index that will be located in the temporary folder.Specify an index to build during execution of the selected short reads aligning algorithm. If this option is selected, the value is <b>required</b>.Specify an index to build during execution of the selected short reads aligning algorithm. If this option is selected, the value is <b>required</b>.......Align optionsAlign optionsOmit reads with qualities lower thanOmit reads with qualities lower thanGenomeAlignerSettingsWidgetGenome aligner settingsGenome aligner settingsFoldersFoldersFolder for built indexesFolder for built indexesQObjectUGENE Genome AlignerUGENE Genome AlignerU2::GenomeAlignerCMDLineTaskRun genome aligner from command lineRun genome aligner from command lineFinished parsing genome aligner options.Finished parsing genome aligner options.Path to reference sequence is not set.Path to reference sequence is not set.Short reads list is empty.Short reads list is empty.Reference (index or sequence) is not set.Reference (index or sequence) is not set. --%1 Use this flag to only build index for reference sequence.
--%1 Use this flag to only build index for reference sequence.
--%1 Path to reference genome sequence
--%1 Path to reference genome sequence
--%1 Path to short-reads data in FASTA or FASTQ format
--%1 Path to short-reads data in FASTA or FASTQ format
--%1 Path to prebuilt index (base file name or with .idx extension). If not set, index is searched in system temporary folder. If --build-index option is applied, index will be saved to specified path.
--%1 Path to prebuilt index (base file name or with .idx extension). If not set, index is searched in system temporary folder. If --build-index option is applied, index will be saved to specified path.
--%1 Path to output alignment in UGENEDB or SAM format (see --%2)
--%1 Path to output alignment in UGENEDB or SAM format (see --%2)
--%1 Memory size (in Mbs) reserved for short-reads. The bigger value the faster algorithm works. Default value depends on available system memory.
--%1 Memory size (in Mbs) reserved for short-reads. The bigger value the faster algorithm works. Default value depends on available system memory.
--%1 Index fragmentation size (in Mbs). Small fragments better fit into RAM, allowing to load more short reads. Default value is 10.
--%1 Index fragmentation size (in Mbs). Small fragments better fit into RAM, allowing to load more short reads. Default value is 10.
--%1 Absolute amount of allowed mismatches per every short-read (mutually exclusive with --%2). Default value is 0.
--%1 Absolute amount of allowed mismatches per every short-read (mutually exclusive with --%2). Default value is 0.
--%1 Percentage amount of allowed mismatches per every short-read (mutually exclusive with --%2). Default value is 0.
--%1 Percentage amount of allowed mismatches per every short-read (mutually exclusive with --%2). Default value is 0.
--%1 Use both the read and its reverse complement during the aligning.
--%1 Use both the read and its reverse complement during the aligning.
--%1 Report only about best alignments (in terms of mismatches).
--%1 Report only about best alignments (in terms of mismatches).
--%1 Omit reads with qualities lower than the specified value. Reads which have no qualities are not omitted. Default value is 0.
--%1 Omit reads with qualities lower than the specified value. Reads which have no qualities are not omitted. Default value is 0.
--%1 Output aligned reads in SAM format. Default value is false.
--%1 Output aligned reads in SAM format. Default value is false.
U2::GenomeAlignerIndexTaskFile %1 is not found. Try to create index another time.File %1 is not found. Try to create index another time.Can not init short reads loader. %1Can not init short reads loader. %1U2::GenomeAlignerPluginUGENE Genome AlignerUGENE Genome AlignerAssembly DNA to reference sequenceAssembly DNA to reference sequenceUGENE Short Reads AlignerUGENE Short Reads AlignerUGENE 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] }
Options
--------
%1
Examples
--------
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
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] }
Options
--------
%1
Examples
--------
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/resultU2::GenomeAlignerSettingsWidgetThis index file is corrupted. Please, load a valid index file.This index file is corrupted. Please, load a valid index file.The index folder has already contain the prebuilt index. But its reference fragmentation parameter is %1 and it doesn't equal to the parameter you have chosen (%2).
Press "Ok" to delete this index file and create a new during the aligning.
Press "Cancel" to change this parameter or the index folder.The index folder has already contain the prebuilt index. But its reference fragmentation parameter is %1 and it doesn't equal to the parameter you have chosen (%2).
Press "Ok" to delete this index file and create a new during the aligning.
Press "Cancel" to change this parameter or the index folder.Set index files folderSet index files folderU2::GenomeAlignerTaskGenome Aligner settingsGenome Aligner settingsIndex file name: %1Index file name: %1Use prebuilt index: %2Use prebuilt index: %2Can not init short reads loader.Can not init short reads loader.The aligning is finished.The aligning is finished.Whole working time = %1.Whole working time = %1.%1% reads aligned.%1% reads aligned.Short-reads loading time = %1Short-reads loading time = %1Results writing time = %1Results writing time = %1Index loading time = %1Index loading time = %1Short-reads IO time = %1Short-reads IO time = %1U2::LocalWorkflow::GenomeAlignerBuildPrompterBuild genome aligner index from %1 and send it url to output.Build genome aligner index from %1 and send it url to output.U2::LocalWorkflow::GenomeAlignerBuildWorkerReferenceReferenceReference sequence url. The short reads will be aligned to this reference genome.Reference sequence url. The short reads will be aligned to this reference genome.Genome aligner index builderGenome aligner index builderGenomeAlignerBuild builds an index from a set of DNA sequences. GenomeAlignerBuild outputs a set of 3 files with suffixes .idx, .ref, .sarr. These files together constitute the index: they are all that is needed to align reads to that reference.GenomeAlignerBuild builds an index from a set of DNA sequences. GenomeAlignerBuild outputs a set of 3 files with suffixes .idx, .ref, .sarr. These files together constitute the index: they are all that is needed to align reads to that reference.IndexIndexOutput index url.Output index url.Reference fragmentationReference fragmentationReference fragmentation sizeReference fragmentation sizeReference sequence URL is emptyReference sequence URL is emptyResult index URL is emptyResult index URL is emptyGenome aligner index building finished. Result name is %1Genome aligner index building finished. Result name is %1U2::LocalWorkflow::GenomeAlignerIndexReaderPrompterRead genome aligner index from %1 and send it url to output.Read genome aligner index from %1 and send it url to output.U2::LocalWorkflow::GenomeAlignerIndexReaderWorkerGenome aligner indexGenome aligner indexResult of genome aligner index builder.Result of genome aligner index builder.Genome aligner index readerGenome aligner index readerRead a set of several files with extensions .idx, .ref, .X.sarr. These files together constitute the index: they are all that is needed to align reads to that reference.Read a set of several files with extensions .idx, .ref, .X.sarr. These files together constitute the index: they are all that is needed to align reads to that reference.IndexIndexSelect an index file with the .idx extensionSelect an index file with the .idx extensionIndex URL is emptyIndex URL is emptyReading genome aligner index finished. Result name is %1Reading genome aligner index finished. Result name is %1U2::LocalWorkflow::GenomeAlignerPrompterunsetunsetAligns reads from <u>%1</u> Aligns reads from <u>%1</u> to reference genome <u>%1</u>. to reference genome <u>%1</u>.U2::LocalWorkflow::GenomeAlignerWorkerIs absolute mismatches values?Is absolute mismatches values?Bowtie2 cannot recognize read pairs from the same file. Please, perform demultiplexing first.Bowtie2 cannot recognize read pairs from the same file. Please, perform demultiplexing first.The slot must be not empty: '%1'The slot must be not empty: '%1'URL of a file with readsURL of a file with readsInput reads to be aligned.Input reads to be aligned.URL of a file with mate readsURL of a file with mate readsInput mate reads to be aligned.Input mate reads to be aligned.Genome aligner dataGenome aligner dataInput reads to be aligned with Bowtie2.Input reads to be aligned with Bowtie2.Assembly URLAssembly URLOutput assembly URL.Output assembly URL.Genome aligner output dataGenome aligner output dataOutput assembly files.Output assembly files.Output folderOutput folderFolder to save UGENE genome aligner output files.Folder to save UGENE genome aligner output files.Output file nameOutput file nameBase name of the output file. 'out.sam' by defaultBase name of the output file. 'out.sam' by defaultReference genomeReference genomePath to indexed reference genome.Path to indexed reference genome.<html><body><p><b>true</b> - absolute mismatches mode is used</p><p><b>false</b> - percentage mismatches mode is used</p> You can choose absolute or percentage mismatches values mode.</body></html><html><body><p><b>true</b> - absolute mismatches mode is used</p><p><b>false</b> - percentage mismatches mode is used</p> You can choose absolute or percentage mismatches values mode.</body></html>Absolute mismatchesAbsolute mismatches<html><body>Number of mismatches allowed while aligning reads.</body></html><html><body>Number of mismatches allowed while aligning reads.</body></html>Percentage mismatchesPercentage mismatches<html><body>Percentage of mismatches allowed while aligning reads.</body></html><html><body>Percentage of mismatches allowed while aligning reads.</body></html>Align reverse complement readsAlign reverse complement reads<html><body>Set this option to align both direct and reverse complement reads.</body></html><html><body>Set this option to align both direct and reverse complement reads.</body></html>Use "best"-modeUse "best"-mode<html><body>Report only the best alignment for each read (in terms of mismatches).</body></html><html><body>Report only the best alignment for each read (in terms of mismatches).</body></html>Omit reads with qualities lower thanOmit reads with qualities lower than<html><body>Omit reads with qualities lower than the specified value. Reads that have no qualities are not omited. <p>Set <b>"0"</b> to switch off this option.</p></body></html><html><body>Omit reads with qualities lower than the specified value. Reads that have no qualities are not omited. <p>Set <b>"0"</b> to switch off this option.</p></body></html>Align Reads with UGENE Genome AlignerAlign Reads with UGENE Genome AlignerUse GPU-optimizationUse GPU-optimization<html><body>Use GPU-calculatings while aligning reads. This option requires OpenCL-enable GPU-device.</body></html><html><body>Use GPU-calculatings while aligning reads. This option requires OpenCL-enable GPU-device.</body></html>Unique UGENE algorithm for aligning short reads to reference genomeUnique UGENE algorithm for aligning short reads to reference genomeShort reads list is empty.Short reads list is empty.U2::ShortReadAlignerCPU[%1] Index size for part %2/%3 is zero, skipping it.[%1] Index size for part %2/%3 is zero, skipping it.U2::ShortReadAlignerOpenCLIndex size for part %1/%2 is zero, skipping it.Index size for part %1/%2 is zero, skipping it.