TASUKE+ multiple genome browser for variants and GWAS

For System phylogenetic tree, (In addition to the previously supported distance matrix format,) it is now possible to create a phylogenetic tree from Newick file. The previous problem "Creating a phylogenetic tree takes a long time for large dataset" has been resolved.

For PrimerDesign's e-PCR function, MFEprimer3 is now supported (in addition to the previously supported MFEprimer2).

For track display, Implemented a function to specify the default genome region to be displayed on first access.

Changed default variant display mode.(One-base unit, SNP+INDEL, No Variant filter)

Some functions have been sped up.

Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added.(it works without them.)

  // Specify a newick file.
  // Recreate the phylogenetic tree quickly by removing Accession leaves from the Newick tree instead of NJ clustering.
  $newickPath = "";

  // For MFEprimer3
  // MFEprimer3 path
  $MFE3path="/PATH/mfeprimer-3.x.x-linux-amd64";
  // MFEprimer3 database fasta path
  $MFE3DBpath="/PATH/reference.fasta";

  // You can set the genome region to display by default.
  // "chr" and "start" are required.
  // "blocksize" and "end" conflict, with "end" taking precedence. If these are not specified, 
  //  the default is "blocksize=1k".
  // [!!!Warning!!!] Since the "start" and "end" positions are automatically changed according
  //  to the number of blocks and "blocksize", they may deviate greatly from the specified positions.
  // chr:       Chromosome/Contig name registered in the DB (excluding prefix(=$chromosome_name))
  // start:     Starting position on the genome.
  // end:       end position on the genome.
  // blocksize: Default is "1k". Please specify one of the following.(1b=1bp, 1k=1000bp)
  // 1b/2b/3b/4b/5b/6b/7b/8b/9b/10b/20b/30b/40b/50b/60b/70b/80b/90b/100b/200b/300b/400b/500b/600b/
  // 700b/800b/900b/1k/2k/3k/4k/5k/6k/7k/8k/9k/10k/20k/30k/40k/50k/60k/70k/80k/90k/100k
  // ex1. array("chr"=>"chr02","start"=>"365001");
  // ex2. array("chr"=>"chr02","start"=>"365001","end"=>"465000");
  // ex3. array("chr"=>"chr02","start"=>"365001", "blocksize"=>"1k");
  $default_position = array("chr"=>"", "start"=>"");

Download: tasuke-plus_20231214.tar 

Changed PHP requirements from "PHP5.0 or later" to "PHP5.3 or later". Any officially supported Linux OS at this time is generally fine.

In this version, we have improved the basic functions mainly for the purpose of being able to browse large dataset(>1000 accessions). See here for recommended server settings.

For Accession Manager, add a function to select Accessions by narrowing down by keywords has been added. The same is true for the Phylogenetic analysis function which has a similar GUI.

For Annotation track, added a function to download gene mRNA, CDS, and Protein sequence(genome sequence was able to download from previous versions)

For SystemTree, added a function to specify the number of leaves to collapse.

For SystemTree, added a function to preview the number of leaves before collapsing when specifying a tree-height threshold.

For Export Variant site (TSV) function, changed the output format to GT notation conforming to multi-sample VCF.

To speed up DB registration, Added scripts to parallelize Variant and Depth registration for each accessions. (tasuke_variant_vcf_multi.pl  tasuke_tsv_db_multi.pl)

For BLAST function, tblastn and tblastx are now supported in addition to blastn. tblastx cannot be selected by default due to its high load. Please enable $useTblastx in the config file to use tblastx.

Speed up some functions.

Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added.(it works without them.)

  // By default, PHPPhylogeneticTrees is used for clustering, but if $phylipDir/exe/neighbor is available, it is mainly used.
  $systreeUsePhylip = 1;
  // For SystemTree ProgressBar. Characters used in progress strings.
  $systreeProgressChar = "*";
  // For SystemTree ProgressBar. Number of $systreeProgressChar to send per cycle of Phylip-neighbor.
  // The larger the number, the smoother ProgressBar, but the larger the amount of data transferred.
  $systreeProgressCharLen = 80;

  //Use TBLASTX (Default:off)
  //tblastx has a high server load. Also, due to the large data size of the result,
  // it may not be possible to store the history to WebStorage (an error will occur).
  // (Even in that case, browsing can be continued)
  $useTblastx = 0;

  // Canvas width for accession ids and groups
  // $title_id_width_rate is the percentage of $accession_cvs_width used to display title(ID).
  $title_id_width_rate = 0.55;

  // Codon table used for AA translation of the "export FASTA" function.
  // The following values can be specified. Default is "standard".
  // standard, bacteria, plastid, protozoa, mold, mycoplasma, spiroplasma, ciliate
  // * [standard, bacteria, plastid] and  [protozoa, mold, mycoplasma, spiroplasma] are each the same table.
  $codontable_type = "";

Download: tasuke-plus_20230901.tar 

Implemented system phylogenetic tree function.

Implemented function to reflect result of the phylogenetic tree sub tool in the system phylogenetic tree.

Implemented function to search and highlight accession on the track.

Implemented cursor lines function.

In AccessionManager, it is now possible to sort with all accession parameters(Variety, Subvariety, Origin, Origin2, Type, Other1, Other2).

Speed up some functions.

Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added.(it works without them, but it is required when using SystemTree)

// [SystemTree] use system tree function.
// Specify a distance matrix file in Phylip format(Lower-triangle matrices).
// https://evolution.gs.washington.edu/phylip/doc/distance.html
// if $distanceMatrixPath is empty or not found, tree function will not be used.
$distanceMatrixPath = "";
// Do you want to display tree by default at startup?
$systreeDefaultOn = 1;

// [System/PhylipTree] Branches whose height is greater than this value will collapsed.
// Float. Invalid if 0 or empty.
$systreeAutoCollapseThreshold = 0;
// What do you consider $systreeAutoCollapseThreshold for? (height/ratio)
$systreeAutoCollapseType = "height";

// [System/PhylipTree] Other options
// - Correction: ""/asec/pow/cdf
$systreeCorrection = "";
// - SortType: height or subtree
//  height : max height of subtree
//  subtree: number of subtree leaves
$systreeSortType = "subtree";
// - SortOrder: ""/asc/desc
$systreeSort = "desc";
// - TreeWidth: int
$systreeWidth = "100";

Download: tasuke-plus_20210831.tar 

Implemented function to color-code variant based on genotype (GT: Homo/Hetero-zygous).

GT:0/0 (reference type homozygous) genotype information can now be registered (disabled by default). This function is effective when DB registering using multi sample vcf (gatkm).

GT:0/0 information can now be displayed on the track when GT color mode was selected.

Speed up some functions.

Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added.(it works without them)

// Placeholder for search form
$placeholder_topsearch = "eg.Os01g0100100-01,chr01:1-100";
$placeholder_possearch = "eg. chr01:1-100";
$placeholder_kwsearch = "(eg. Os01g0100100-01)";

Download: tasuke-plus_20201117.tar 

Improved function to display GT:1/2 variant.

Implemented function to highlight variants for specific gene.

Implemented function to filter variants by SnpEff Impact level.

Supports registration of a large number of Chr/Contig reference seqs. ( >1000)

Speed up some functions.

Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added .(it works without it, but it is required when registering a large number of Chr/Contig reference seqs)

// Whether to automatically determine if the table is divided or not?
$autoDetectSerialTable = 0;

Download: tasuke-plus_20200928.tar 

Implemented the function to highlight the searched genomic region.

Implemented the function to display Blast result on Track.

Improved so that different external links can be set for each tracks.

Speed up some functions. Several Bug fixes.

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters in "tasuke_www/conf/config.php" have been added.(it works without them)

// External links for each tracks
// The value set here has priority over $external_link/$external_link_tag_gff/$external_link_suffix.
$external_sites = array();

Download: tasuke-plus_20200305.tar 

Change webStorage from localStorage to sessionStorage

Speed up some functions

Several Bug fixes

There are no DB schema changes since TASUKE+ first version(20180720).

There are no parameters added to "tasuke_www/conf/config.php" since the previous version.

Download: tasuke-plus_20190826.tar 

Improvement:create GWAS manhattan plot when opening GWAS dialog.
You can use many functions on GWAS manhattan plot.
Please see GWAS function page.

Improvement:get fasta and create phylogenetic tree faster.
You can get fasta and create phylogenetic tree on a few seconds.

Improvement:Import variant information with snpEFF ANN feature.
You can import variant information with snpEFF ANN feature on TASUKE database.

Several Bug fixes

There are no DB schema changes since TASUKE+ first version(20180720).

The following parameters have been added to "tasuke_www/conf/config.php".(it works without them)

//set the number of threads (default:4)
//To set more threads , get fasta sequence and phylogenetic tree faster.
//usage: If you use 3 threads;
$threadnum = "4";

//gene id column number
//To get geneid information on ANN/EFF information, set column number.
//If you can't get correct information on SNP detail information , change
//correct number.
$ANNcol = 6;
$EFFcol = 8;

Download: tasuke-plus_20190328.tar 

New feature GWAS track
Create GWAS track with your GWAS data.

Improvement:Implemented the ePCR option for Primer prediction.
Using this option, you can check the specificity of primers predicted by primer3

Several Bug fixes

There are DB schema changes since TASUKE 1.5.1. If you are upgrading from legacy TASUKE, run the script "tasuke_bin/tasuke_update_for_gwas.pl".

Do not reuse legacy TASUKE's "tasuke_www/conf/config.php", but use the one in this package.

Download: tasuke_plus_20180720.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