Aquileo | Recent changes to wiki

Aquileo | Home modified by Alexey Gurevich

Tue, 26 Nov 2024 07:30:13 -0000

--- v65
+++ v66
@@ -1,49 +1,4 @@
-####26 May 2016####
-
-**QUAST 4.1** is released! Icarus visualizations are even better now!
-
-In addition to the new release, we also moved to a new website. From now on, all news and the most up-to-date QUAST info will be placed at http://quast.sf.net/. Stay tuned!
-
-[[download_button]]
-
-

-**Quick links**:  
-Full Manual (including Install and FAQ)
-License
-Changes
-
-*Web-based* QUAST
-QUAST news and info website (including pages for MetaQUAST, Icarus and QUAST itself).
-QUAST source code at Github: command-line tool, web interface.
-
-

-####1 April 2016####
-Bioinformatics published MetaQUAST paper in Volume 32, issue 7 (Pp. 1088-1090)! 
-You can download citation in various formats here.
-
-####27 November 2015####
-* QUAST 3.2 was released including reads support for structural variation detection (based on Manta).
-
-####June 2015####
-* The number of QUAST downloads exceeded ten thousands!
-* QUAST repositories are open for public access on Github! Command-line tool is here, web interface is here.
-

-
-####17 June 2013####
-QUAST paper has been selected for F1000Prime!
-
-
-####15 April 2013####
-Bioinformatics published QUAST paper in Volume 29, issue 8 (Pp. 1072-1075)!
-You can download citation in various formats here.
-
-#####Other useful information:#####
-
-We will be thankful if you help us make QUAST better by sending your comments, bug reports, and suggestions
-to quast.support@bioinf.spbau.ru.
-
-
-QUAST team,
-Algorithmic Biology Lab.
+The latest info is at the QUAST website: http://quast.sf.net/
+Detailed manual for the latest version is also there: https://quast.sf.net/manual.html 
+For issues, please use our GitHub tracker: https://github.com/ablab/quast/issues
+For other questions, please write to Dr. Alexey Gurevich: alexey.gurevich@helmholtz-hips.de

Aquileo | Home modified by Alexey Gurevich

Fri, 27 May 2016 09:45:47 -0000

--- v64
+++ v65
@@ -13,7 +13,7 @@
 Changes

 *Web-based* QUAST
-QUAST page at Algorithmic Biology Lab website (see also MetaQUAST and Icarus pages).
+QUAST news and info website (including pages for MetaQUAST, Icarus and QUAST itself).
 QUAST source code at Github: command-line tool, web interface.

Aquileo | Home modified by Alexey Gurevich

Fri, 27 May 2016 09:43:23 -0000

--- v63
+++ v64
@@ -1,8 +1,8 @@
-####19 April 2016####
+####26 May 2016####

-**QUAST 4.0** is released! Now with Icarus visualizations!
+**QUAST 4.1** is released! Icarus visualizations are even better now!

-Icarus is a novel genome visualizer for *de novo* genome assemblies. It is embedded into QUAST and MetaQUAST pipelines. See http://bioinf.spbau.ru/icarus for details and examples of its output. QUAST 4.0 also includes many other features and fixed bugs, see Changes for the full list.
+In addition to the new release, we also moved to a new website. From now on, all news and the most up-to-date QUAST info will be placed at http://quast.sf.net/. Stay tuned!

 [[download_button]]

Aquileo | Home modified by Alexey Gurevich

Tue, 19 Apr 2016 12:19:26 -0000

--- v62
+++ v63
@@ -1,8 +1,8 @@
-####27 November 2015####
+####19 April 2016####

-**QUAST 3.2** is released! Now with reads support!
+**QUAST 4.0** is released! Now with Icarus visualizations!

-New type of input data is added: raw reads (experimental feature!). They are used for detecting structural variants (SV) between reference genome and sequenced organims. Found SV are used for masking related misassemblies. In addition, reformatted and more portable HTML reports, new options and new type of misassemblies are added. See Changes for the full list of new features and fixed bugs.
+Icarus is a novel genome visualizer for *de novo* genome assemblies. It is embedded into QUAST and MetaQUAST pipelines. See http://bioinf.spbau.ru/icarus for details and examples of its output. QUAST 4.0 also includes many other features and fixed bugs, see Changes for the full list.

 [[download_button]]

@@ -10,22 +10,24 @@
 **Quick links**:  
 Full Manual (including Install and FAQ)
 License
-Changes
+Changes

 *Web-based* QUAST
-QUAST page at Algorithmic Biology Lab website
+QUAST page at Algorithmic Biology Lab website (see also MetaQUAST and Icarus pages).
+QUAST source code at Github: command-line tool, web interface.

 

-####26 November 2015####
-* Bioinformatics published MetaQUAST paper (Advance Access). You can find more details about MetaQUAST and examples at  MetaQUAST page. 
+####1 April 2016####
+Bioinformatics published MetaQUAST paper in Volume 32, issue 7 (Pp. 1088-1090)! 
+You can download citation in various formats here.

-####7 July 2015####
-* Long-awaited QUAST 3.0 was released including multiple novel stuff especially for metagenome assemblies.
+####27 November 2015####
+* QUAST 3.2 was released including reads support for structural variation detection (based on Manta).

 ####June 2015####
 * The number of QUAST downloads exceeded ten thousands!
-* QUAST repositories are open for public access on Github! Command-line tool is here, web interface is here. Any feedback is welcomed at quast.support@bioinf.spbau.ru!
+* QUAST repositories are open for public access on Github! Command-line tool is here, web interface is here.
 


 ####17 June 2013####
@@ -37,13 +39,6 @@
 ijkey=Kzq9lhMayiqecq9&keytype=ref">Pp. 1072-1075)!
 You can download citation in various formats here.

-#####The latest version details:#####
-
-QUAST version is released under GPL v2 (see LICENSE for details). Note that some of build-in third-party tools are not under GPL v2. See LICENSE for details.
-
-See Changes for a full list of new features and fixed bugs. We tried to support all your requests sent to quast.support@bioinf.spbau.ru in this version!
-Detailed instructions on QUAST running and understanding its output are given in the Manual.
-
 #####Other useful information:#####

 We will be thankful if you help us make QUAST better by sending your comments, bug reports, and suggestions

Aquileo | Changes modified by Alexey Gurevich

Fri, 27 Nov 2015 15:04:54 -0000

--- v20
+++ v21
@@ -1,4 +1,41 @@
 ###Version history###
+
+####3.2####
+1\. The tool now accepts raw reads for improving quality assessment (experimental feature, try with care):
+   - reads should be provided with --reads1 (or -1), --reads2 (or -2) options,
+   - reads are aligned to reference genome using bowtie2 (embedded),
+   - Manta structural variation (SV) calling tool (embedded) is run on bowtie2 output,
+   - found SVs are used for classifying QUAST misassemblies into true ones and fake
+         ones (caused by structural differences between reference sequence and
+         sequenced organism). Fake misassemblies are excluded from "# misassemblies" metric
+         and reported in novel "# structural variants" metric.
+
+2\. HTML reports content reformatted, especially in MetaQUAST reports:
+   - GC % and all metrics based on genome length (NG50, NGA50, LGA75, etc) are excluded
+         from the combined reference statistics (they don't make sense there);
+   - N50 is replaced with more fair and comparable metrics such as "Total length >= 1000 bp",
+         "Total length >= 10000 bp" in the main MetaQUAST report. Extended version still has N50.
+   - N50 is also hidden in single-genome QUAST reports and exposed NGA50 instead.
+
+3\. Scaffold gap size misassemblies are introduced. They are reported only when --scaffolds  is used.
+
+4\. Several new options added:
+   - "--memory-efficient" for running QUAST with minimal memory consumption (but much slower)
+   - "--test-sv" for testing structural variants mode (see 1.)
+   - "--silent" for minimal output to stdout (full verbose output is saved in the logs anyway)
+
+5\. MetaQUAST output directory content is reformatted. Per reference reports are saved
+         inside the directory <output_dir>/runs_per_reference, summary reports are under summary directory.
+         The only top-level files are metaquast.log and report.html (summary HTML report with links to all subreports).
+
+6\. Colors in HTML reports and PDF/PNG plots are synchronized, now they are the same
+         for the same assemblies.
+
+7\. Additional check for Matplotlib v1.1 (needed for drawing PDF/PNG plots since QUAST v3.1)
+
+8\. Fixed several minor and major bugs.
+
+9\. Citation for MetaQUAST paper added.

 ####3.1####
 1\. MetaQUAST:

Aquileo | Home modified by Alexey Gurevich

Fri, 27 Nov 2015 14:59:32 -0000

--- v61
+++ v62
@@ -1,10 +1,10 @@
-####25 August 2015####
+####27 November 2015####

-**QUAST 3.1** is released! Even better, faster, and much lighter than QUAST 3.0!
+**QUAST 3.2** is released! Now with reads support!

-Significantly reduced size of the installation package, upgraded MetaQUAST including Krona charts, heatmaps for HTML reports, and a lot of other features and bug fixes included.
+New type of input data is added: raw reads (experimental feature!). They are used for detecting structural variants (SV) between reference genome and sequenced organims. Found SV are used for masking related misassemblies. In addition, reformatted and more portable HTML reports, new options and new type of misassemblies are added. See Changes for the full list of new features and fixed bugs.
+
 [[download_button]]
-
 See details about new features and MetaQUAST in the manual.

 

 **Quick links**:  
@@ -16,8 +16,9 @@
 QUAST page at Algorithmic Biology Lab website

 

-####20 August 2015####
-* MetaQUAST paper was submitted to *Bioinformatics*. You can find more details and examples at  MetaQUAST page. Current version of the citation is also there.
+####26 November 2015####
+* Bioinformatics published MetaQUAST paper (Advance Access). You can find more details about MetaQUAST and examples at  MetaQUAST page. 

 ####7 July 2015####
 * Long-awaited QUAST 3.0 was released including multiple novel stuff especially for metagenome assemblies.

Aquileo | Home modified by Alexey Gurevich

Tue, 25 Aug 2015 16:22:16 -0000

--- v60
+++ v61
@@ -16,6 +16,9 @@
 QUAST page at Algorithmic Biology Lab website

 

+####20 August 2015####
+* MetaQUAST paper was submitted to *Bioinformatics*. You can find more details and examples at  MetaQUAST page. Current version of the citation is also there.
+
 ####7 July 2015####
 * Long-awaited QUAST 3.0 was released including multiple novel stuff especially for metagenome assemblies.

@@ -35,7 +38,7 @@

 #####The latest version details:#####

-QUAST version 3.0 is released under GPL v2 (see LICENSE for details). Note that some of build-in third-party tools are not under GPL v2. See LICENSE for details.
+QUAST version is released under GPL v2 (see LICENSE for details). Note that some of build-in third-party tools are not under GPL v2. See LICENSE for details.

 See Changes for a full list of new features and fixed bugs. We tried to support all your requests sent to quast.support@bioinf.spbau.ru in this version!
 Detailed instructions on QUAST running and understanding its output are given in the Manual.

Aquileo | Changes modified by Alexey Gurevich

Tue, 25 Aug 2015 16:17:24 -0000

--- v19
+++ v20
@@ -1,4 +1,34 @@
 ###Version history###
+
+####3.1####
+1\. MetaQUAST:
+   - more specific algorithm for reference searching and downloading, particularly
+         only Bacteria and Archaea are downloaded;
+   - Krona charts are added for showing taxonomic profile based on found references;
+   - metric-level and misassemblies plots are added to summary HTML report;
+   - better structure for text reports and plots in summary folder.
+
+2\. Significantly reduced size of the installation package. This is done by removing
+         BLAST binaries which are needed only for MetaQUAST run without references. On the
+         first such run, BLAST binary for target OS will be automatically downloaded.
+
+3\. Heatmaps added to HTML reports.
+
+4\. Separate install.sh and more complex install_full.sh scripts for installing regular
+         versions of QUAST and MetaQUAST or extended one (with ability to run MetaQUAST without
+         reference genomes).
+
+5\. New option "--plots-format" for selecting output format for plots (PDF by default).
+
+6\. Default number of threads changed from 100% CPUs to 25% of CPUs.
+
+7\. Changes in one-letter options, including replacing confusing -T to -t for --threads
+         and -M to -m for --min-contig.
+
+8\. Skipping broken version of scaffolds from analysis if they are equal to original
+         ones (see --scaffold option for details).
+
+9\. Fixed several minor bugs.

 ####3.0####
 1\. Significant changes in MetaQUAST functionality:

Aquileo | Home modified by Alexey Gurevich

Tue, 25 Aug 2015 16:13:26 -0000

--- v59
+++ v60
@@ -1,8 +1,8 @@
-####7 July 2015####
+####25 August 2015####

-Long-awaited **QUAST 3.0** is released! Welcome brand new version of our tool.
+**QUAST 3.1** is released! Even better, faster, and much lighter than QUAST 3.0!

-Significantly upgraded MetaQUAST, new options and new colorful plots, mighty speed up, and a lot of other features included.
+Significantly reduced size of the installation package, upgraded MetaQUAST including Krona charts, heatmaps for HTML reports, and a lot of other features and bug fixes included.
 [[download_button]]
 
 See details about new features and MetaQUAST in the manual.

@@ -16,6 +16,9 @@
 QUAST page at Algorithmic Biology Lab website

 

+####7 July 2015####
+* Long-awaited QUAST 3.0 was released including multiple novel stuff especially for metagenome assemblies.
+
 ####June 2015####
 * The number of QUAST downloads exceeded ten thousands!
 * QUAST repositories are open for public access on Github! Command-line tool is here, web interface is here. Any feedback is welcomed at quast.support@bioinf.spbau.ru!

Aquileo | Home modified by Alexey Gurevich

Mon, 13 Jul 2015 09:36:16 -0000

--- v58
+++ v59
@@ -4,7 +4,7 @@

 Significantly upgraded MetaQUAST, new options and new colorful plots, mighty speed up, and a lot of other features included.
 [[download_button]]
-See details about new features and MetaQUAST in the manual.
+
 See details about new features and MetaQUAST in the manual.

 

 **Quick links**: