QUAST 5.3.0

QUAST 5.3.0 is officially the first release that supports only Python 3 and 64-bit Linux/macOS. While some legacy code remains, we will gradually remove it in future updates. Functionally, this version is equivalent to v.5.2.0; however, several critical bugs have been fixed, and some embedded tools have been updated. See the complete list of changes here.

Most notable features/changes:

• Updated embedded minimap2 to the latest release, v2.28 (alignment results remain unchanged).
• Resolved crashes on macOS with Python 3.8+ (see #175).
• Fixed occasional crashes related to Krona charts in MetaQUAST's no-reference mode (see #251). A new --no-krona option has been added to complement other speed-up options.
• Updated documentation and support contact information following the full transition of QUAST maintenance and development to the Gurevich Lab at HIPS/HZI.

QUAST 5.2.0

QUAST 5.2.0 includes everything included in the 5.1.0 release candidate (which was never fully released) and many additional novelties and bug fixes. See the full list of changes here.
Note: v.5.2.0 is supposedly the last release with Python 2 support and many legacy code.

The most notable features/changes:

• Core alignment changes (might affect all alignment-based metrics!): embedded minimap2 aligner updated to 2.24, default alignment parameters slightly changed
• New metrics: auN, auNG, auNA, auNGA (areas under the Nx/NGx/NAx/NGx curves), for more detail see the Heng Li blog post
• New options: --local-mis-size for setting minimal size of a local misassembly (default changed from 85 to 200) and --report-all-metrics for keeping all quality metrics (even not applicable for the run) in the main report
• Substantial speed up of the Best-Set-Selection algorithm (first introduced in the QUAST-LG paper)

QUAST 5.1.0rc1

This is a pre-release of the upcoming v.5.1.0. All changes are here. Detailed release notes are here (this kind of document is created for the first time in the QUAST release history!)

The most notable features/changes:

• New option --reuse-combined-alignments (MetaQUAST only) for reusing alignments against the combined_reference in the subsequent runs_per_reference analysis stages
• Other changes in MetaQUAST pipeline: improved no-ref mode, default min IDY set to 90%
• New option --x-for-Nx for reporting Nx, Lx, etc metrics for a specific value of x in addition to N50, L50, etc. The default value is 90. The previous non-changeable default was 75
• Updates in embedded tools -- SILVA (v138 now), BUSCO (fixed links to v3/odb9), GeneMark (updated licenses)

QUAST 5.0.2

A bugfix release:

• Fixed bug with missing genome features reference stats and plot in report.html
• Fixed bug related to newest versions of joblib (0.10 and higher)
• Fixed bug with some rare crashes of the reads_analyzer module

QUAST 5.0.1

Mostly a bugfix release:

• Fixed bug in using --split-scaffolds with MetaQUAST
• Fixed bug in parsing genome sequences of GeneMark predicted genes
• Fixed bug with crash of UpperBound creation when no paired-end reads are provided

Few updates that do not affect QUAST functionality:

• Improved documentation and error/warning/info messages
• Trying to use already installed minimap2, Glimmer, joblib, simplejson rather than distributions from the QUAST package (important for external QUAST installers)
• GeneMark license files are updated

And just two tiny functional changes:

• Using asm20 minimap2 preset for references with high divergence from the assembled organism (provided --min-identity is below 90%). As before, asm10 is used for --min-identity below 95% and asm5 for 95% and above
• Now FASTA entry names are considered as a sequence before the first space in the header line (>...). Previously, the entire lines were considered.

QUAST 5.0.0

QUAST 5.0.0 includes many features and fixed bugs, see the full list of changes here.

The most notable new feature is QUAST-LG mode (LG stands for "large genomes"). Now the tool can evaluate large-scale genome assemblies in a reasonable time (e.g., human assemblies in just a few hours). Significant speedup was achieved by both use of new fast aligner (minimap2) and the refactoring of alignment analyzing modules. We also introduced several new metrics suitable for large genomes but applicable to smaller organisms as well (e.g., k-mer-based completeness and correctness; the number of BUSCO genes; etc). The last but not the least, we developed the concept of upper bound assembly for a given genome and set of reads (theoretical limits on the assembly completeness and contiguity).

See http://cab.spbu.ru/software/quast-lg/ and our ISMB 2018 proceeding paper for more details on QUAST-LG and examples of its application to real datasets.

QUAST 4.6.3

Bugfix release (mostly covers problems erroneously introduced in v4.6.2)

• Fixed crash of quast.py --test (introduced in v4.6.2).
• Fixed crash of BSS in MetaQUAST mode (introduced in v4.6.2).
• Proper float/integer division in both Python2 and Python3 (may affect the number of scaffold gap size misassemblies in Python2).

QUAST 4.6.2

Bugfix release:

• Fixed relatively rare bug of BSS when using large --min-alignment (> 500, if you used the default value of 65 you are fine with 4.6.0 release).
• Improved check of previously generated results before reusing them (also rarely occurring problem).
• GeneMark licence files are updated.

QUAST 4.6.1

Bugfix release: fixed few minor problems preventing QUAST v.4.6 installation via third-party providers (pip and bioconda).
Note: There is no new features or bugfixes related to QUAST functionality in v.4.6.1, so if you are on v.4.6.0 already, there is absolutely no need to update to v.4.6.1. Please wait for our next major release!

QUAST 4.6.0

Python 3.6 support, significant speed up on complex assemblies, and a few small but important bug fixes found by our beloved users!

For the full list of new features and fixed bugs, see http://quast.bioinf.spbau.ru/CHANGES.