TASUKE multiple genome browser

Bug fix: Security fixes.

Download : tasuke_tools_1.5.3.tar 

Bug fix: Security fixes.

Bug fix: You can get the csv data about the SNP in geneID you selected in Exporting CSV dialog.

Download : tasuke_tools_1.5.2.tar 

Change: The description of Row column options on Track manager is changed from "1" and "4" to "fold" and "expand".

Bug fix: Function of phylogenetic tree analysis on Tools was fixed.

Bug fix:"|(pipe)" is usable in GFF file used for visualization of annotation track table.

Download : tasuke_tools_1.5.1.tar 

New feature: Multiple conditions for the general purpose track
Set multiple condition data to general purpose track of each accession, and this feature shows the data by multiple rows on each accession. Users can be show a time series or tissue data on TASUKE.

Change: You can set any colors to each accession group.

Change: A progress bar was added for wait time of loading the top-page.

Change: View of accession name and group. Letters of accession name/group that are beyond the canvas and the letters are automatically trimmed. And '~' will be added to that tail.

Bug fix: Incorrect group names were generated by phlogenetic analysis.

Bug fix: Content of VCF and GFF file have " or ', installation process was failed.

Bug fix: Sometime, any block detail information shows incorrect contents.

Bug fix: Environment of user-side is automatically loaded when configuration file of server-side was changed.

Download : tasuke_tools_1.5.0.tar 

New feature: Phylogenetic analysis
Making phylogenetic tree from any genomic region. Set transcript id to the dialog window, you can get a tree from CDS region. In addition, you can get order of accessions sorted based on the phylogenetic tree.(PHYLIP software is required for use the feature.)

New feature: Cacheing system using Redis (beta)
tasuke_cuffdifftoGFF.pl: It converts result of cuffdiff to GFF file. Set the file to the database, significant region will be highlighted.

New function: Cuffdiff to GFF
tasuke_sort_by_distance.pl: This tool make a file for order of accessions. It has 2 method for getting genetic distance. Copy the file to /TASUKE_HOME/conf/, then the order of accessions is sorted based on the file.

New function: Creating order of accessions by genetic distance
PHYLIP dnadist: Sorting by a phylogenetic tree from result of PHYLIP.

New function: Upload/download order of accessions by using accession manager

New function: Automatic installation tool
This tool automatically detects dataset for TASUKE. And it loads any dataset to the database.

New function: Selecting accession from external webpage
Set destination accessions to a localstorage, these accessions only appear.

Improvement: Support for Oracle database
For more reliability and high performance, you can use Oracle database as backend database. We recommends oracle database version 11 or later. If you have enterprise edition, you can use a scripts for database compression.

Improvement: Support for snpEff 4.x
Run snpEFF with '-classic' and '-formatEff' options.

Improvement: More robust security

Improvement: Compressed web storage
The real local storage capacity is changed 5 MB to 15 MB. And it can accept about 3000 accessions.

Change: Detail window from annotation track
Click on a GFF object on annotation track, detail window appears.

Change: In tasuke_init.pl and tasuke_accession.pl, you can terminate these installation process by 'ctrl+c'.

Change: Additional messages for install process.

Bug fix: Contents height was incorrect in a certain case.

Several tiny bug fixes.

Download : tasuke_tools_1.4.0.tar 

Bug fix: Generating a FASTA file feature did not work in some condition.

For update 1.3.0 to 1.3.1, copy the tasuke_www/js/dialog.js to your TASUKE directory (TASUKE_HOME/js/dialog.js).

Download : tasuke_tools_1.3.1.tar 

New feature: General purpose track (Custom track)
TASUKE can accept BAM, BED and BEDGraph file as general purpose track for various NGS analysis data.

New feature: Partitioned data transmission
It loads visible accession only on a web browser. Scroll the browser, it automatically loads from database. However, invisible accessions does not load. This feature reduced loading time, and it can accept a lot more accessions.

New feature: Color manager for each data
You can set color definition and gradient for each data.

New feature: Browser cache collision avoid system

New feature: Moving to the destination region by URL parameter

New feature: More detail setting for external link on the annotation track

New feature: Feature IDs on the annotation track are always viewed or not
Turning on this mode, it shows the feature IDs below the object. This mode will be turned off when the IDs collision is occured.

New feature: Sorting the accessions on the accession manager
Click the tabs on accession manager, and the accession list is sorted.

New feature: A database schema upgrading tool.
When you want to update the TASUKE, run this tool for upgrading the database schema. After this processing is finished, you can use the new features.

Change: Reference sequence name is always viewed

Change: Index of an annotation track table

Bug fix: Page scrolling on a web browser collisioning with mouse event of the TASUKE

Bug fix : Creating TSV file was failed when a BAM file does not include read mapped registered sequence.

Several tiny bug fixes.

Download : tasuke_tools_1.3.0.tar 

New feature: Primer designing
You can get primer pairs and the sequences for designing primer on a Primer3 web interface. This feature requires Primer3 (version 2.3.0 or later) on your server. And set the primer3 path to the configuration file (conf/config.php).

There are two ways for primer designing.
menu:tool => PRIMER3 => Set parameter => primer designing
A variant site on the block => pick primer => Set parameter => primer designing

Moving position to the destination region became easier to work.

A variant detail information became easy to see.

Bug fix : Creating a depth file.

Bug fix : Loading a reference sequence was failed when the name includes white space.

Bug fix : Nothing was Loaded when a VCF file has the unregistered chromosome.

Bug fix : When the number of accessions is less than 5, top menus were hidden by a SNP density object.

Bug fix : A block size indicator chases the scroll position on the browser.

Download : tasuke_tools_1.2.0.tar 

New feature: Moving to destination region by Drag and Drop on the position meter.

New feature: An animation was added when the loading data from database.

Improvement: Loading time from a database was significantly reduced.

Changes : A depth file is not required for viewing detail information.

Download : tasuke_tools_1.1.0.tar 

New feature: Showing each variants by real position.
It came to be able to show each variants variants by real position. You can see that by clicking on frequency button of view mode on the top menu.

New feature: Searching annotations by keyword
You can search annotations by keyword. Search results appears on dialog box. The function uses ID and Note tag in GFF file which is target of search. *If you want to use this function, try running tasuke_track.pl(in this version) again.

New feature: Accession management tool is become flexible.
[tasule_init.pl] : This tool initialize database for TASUKE.
[tasuke_accession.pl] : This tool has 3 functions. Addition of accession, updating accession information and deleting accession.

New feature: Fine tunable zoom level.

New feature: New feature : Order of the accessions
You can change the order of accession by writing accession_no on "order.conf".

New feature: Moving to a destination region by Drag and Drop on the position meter.

New feature: An animation was added when the loading data from database.

Improvement: Loading time from a database was significantly reduced.

Changes: A depth file is not required for viewing detail information.

Download : tasuke_tools_1.0.0.tar 

Bug fix: When you click a SNP/INDEL block, you could not view a part of detail informations.

Download : tasuke_tools_0.8.4.tar 

Bug fix: Maximum of depth value was disabled.

Download : tasuke_tools_0.8.3.tar 

Improvement : A depth installation tool
The new install process is 3 to 10 times faster than "tasuke_depth_vcf.pl".
[tasuke_bamtodepth.pl] : Convert a bam file to the tsv formatted file(depth information for the MySQL database).
[tasuke_depth_db.pl] : Install a tsv formatted file in MySQL database using this tool.

Change: The controller, variant filter and indicator for depth and variants are integrated into floating box.

Change: Added an option for the "Export FASTA". The option can be set line width.

Change: Added a dialog box for "Change reference" function.

Bug fix: Blank line at beginning of the download file.

Bug fix: Background color and canvas are broken when horizontal scrolling.

Download : tasuke_tools_0.8.2.tar 

New feature : Export by fasta file
The fasta file being exported shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous". Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set.

Changes: Added a "GO" button on the Search & Jump dialog.

Bug fix: Display of insertion sequence on the view of 1bp Scale.

Bug fix: Reverse complement of the reference sequence.

Bug fix: A message of search by postion or annotation ID.

Download : tasuke_tools_0.8.1.tar 

This is the first release of TASUKE.

Download : tasuke_tools.tar