-- 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:
       - if no references are provided, MetaQUAST downloads references from NCBI database
         based on best hits of assemblies alignments vs SILVA 16S rRNA database 
         (included in QUAST package);
       - multiple summarising reports are added: plots and text tables for each metric 
         (all assemblies vs all references in one file), histograms of # misassemblies 
         per reference for all assemblies separately, summary HTML-report with all metrics 
         per each assembly and each reference (expandable lines);
       - new metrics: interspecies translocations and # possibly misassembled contigs;
       - fixed handling of reference with more than one entry in FASTA file 
         (chromosome plus plasmids or multiple chromosomes);
       - option --reference now accepts directory (takes all references from this dir);
       - fixed handling of closely related species by using --ambiguity-usage 'all' on 
         combined reference run.
       
      2. Speed ups:
       - 5x-100x speed up in case of running QUAST without reference;
       - processing of large (> 50 Mbp) multi-chromosome references in parallel (per chromosome);
       - new speed up options: --no-check, --no-gc, --no-snps, --fast (a combination of other).

      3. More reports about misassemlies (in <output_dir>/contigs_reports/): 
       - misassemblies_plot.pdf with histogram of misassembly types distribution per assembly.
       - contigs_report_<assembly_name>.mis_contig.info with brief details about misassembled 
         contigs only. 

      4. Improved and updated misassemblies detection algorithm:
       - more accurate algorithm for processing multiple ambiguous alignments;
       - using --ambiguity-usage value for processing internal overlaps between adjacent aligned
         blocks of a misassembled contig;
       - marking of local misassemblies with small inconsistency (<= 85 bp) as fake misassemblies
         (indels or mismatches) if gap on the contig is filled mostly with Ns;
       - option --extensive-mis-size/-x to set extensive misassembly size, i.e. min inconsistency
         size for relocations (default is 1000 as earlier);
       - option --min-alignment/-i to set minimum alignment length (Nucmer's parameter), default
         is 0.

      5. Fixed HTML-reports issues:
       - Y-axis coordinates on plots interactive hangover tooltips;
       - NAx plot small bug.

      6. GeneMark-ES is used for predicting genes in eukaryotic genomes instead of Glimmer-HMM.
      For using Glimmer-HMM, a new option --glimmer added.

      7. GeneMarkS incorporation fixed. Previously it was run on predifined heuristic models based 
      on GC content. Now it uses self-training module for getting the correct model.
      
      8. Fixed several minor bugs.

      9. GeneMark licenses updated.

      10. Updated LICENSE (third-party tools details) and Manual.


2.3   1. Changed logic in misassembly computation. Fixed several minor bugs in misassembly
      detection algorithm and one major bug caused by linear represenation of circular
      references and contigs in fasta format.

      2. Added contig alignment plots. See details in manual and in the QUAST paper (Fig. 1)

      3. Genome analyzer module (computation of genome fraction, duplication ratio,
      number of genes and operons) is parallelized.

      4. Option --test became an installation util analogue. It compiles all required binaries and 
      checks correctness of QUAST and MetaQUAST execution on test datasets.

      5. Former plots.pdf upgraded with report tables and renamed to report.pdf. Now it is 
      a file with all tables and plots generated by QUAST.

      6. A new option --no-plots added for speeding up computation if plots are not needed.
    
      7. GeneMark license updated, instructions for manual updating added.

      8. Generation of misleading single-columns histograms removed (when only single assembly
      file was specified).

      9. More error and exception handlers added.

      10. Fixed bug with indel counting (caused slightly overestimated indels rate in some cases).
      
      11. Fixed several minor bugs.
       
      12. Code refactored.


2.2   1. The tool now supports metagenomic assemblies. It accepts multiple references
      and produces several reports:
       — for all contigs and all input genomes merged into one,
       — separate reports for only contigs aligned to a particular genome,
       — for the contigs not aligned to any reference provided.

      Usage:
         metaquast.py contigs_1 contigs_2 ... -R reference_1,reference_2,reference_3,...

      All other options for metaquast.py are the same as for quast.py.

      2. MetaGeneMark is used to find genes in metagenomic assemblies.
      In metaquast.py by default, in quast.py with --meta option.

      3. In place of --allow-ambiguity, a new option --ambiguity-usage (-a) introduced.
      The new option lets specify a way to process ambiguous regions:
      -a one, -a all or -a none.

      4. A new option --labels (or -l) allows to provide human-readable assembly names.
      Those names will be used in reports, plots and logs, instead of file names.
      For example:
         -l SPAdes,IDBA-UD

      if your labels include spaces, use quotes:
         -l "SPAdes 2.5, SPAdes 2.4, IDBA-UD"

         -l SPAdes,"Assembly 2",Assembly3

      5. Minor improvements of HTML reports.

      6. Fixed bugs in misassemblies detection algorithm.


2.1   Option --strict-NA added to control computation of NAx/NGAx metrics. 
      This option forces QUAST to break contigs by any misassembly event, 
      including local misassemblies (like in v.2.0). By default, QUAST v.2.1
      breaks contigs only by extensive misassemblies to compute NAx/NGAx 
      (like in v.1.*).

      Improvement of indels computation. QUAST now counts consecutive single nucleotide
      indels as one indel. Total length of all indels is also reported (equal to
      # indels metric evaluated with previous versions). Short (<= 5 bp) and long (>5 bp)
      indels are reported.

      Option --est-ref-size added to set estimated reference size for computing NGx 
      metrics in case a reference genome is not available.

      GAGE mode is parallelized.

      Fixed bugs in misassemblies detection algorithm.

      Fixed bugs in SNPs detection algorithm.

      Fixed bugs in processing circular chromosomes (affects Genome fraction, # genes,
      # operons).

      Fixed several minor bugs.


2.0   Significantly improved assessment of large genomes. Current limit on size of a
      reference genome is 536 Mbp PER CHROMOSOME instead of 536 Mbp TOTAL in the
      previous versions. Alignment to different chromosomes is performed in parallel.

      Changes in algorithm for evaluating Genome fraction, # genes and operons.
      Filtration of short, ambiguous, and redundant alignments is performed before
      the evaluation. Option --use-all-alignments is added for compatibility
      with 1.* versions.

      New algorithm for finding SNPs and indels.

      Ability to change colors, line styles, etc. in plots and content, metric names
      in reports.

      GlimmerHMM for predicting genes in eukaryotes.

      Gene Finding is parallelized and its run is controlled by --gene-finding option.

      Improvement of HTML-reports and plotting units.

      Fixed several bugs.

1.3   QUAST is now a multi-threaded tool: the most time-consuming step (alignment to
      a reference genome) is computed in parallel.

      A MacOS version of GeneMark.

      Significantly improved HTML-reports.

      More informative error messages.

      A simple logic for evaluating scaffolds.

      New metrics: duplication ration and largest alignment.

      More careful counting of misassemblies.

      Min contig threshold changed from 200 to 500.

      Fixed several bugs.


1.2   Indels and N's counting.

      More detailed statistics on misassemblies (classification in inversions,
      relocations, translocations, local misassemblies).

      More detailed statistics on partially unaligned contigs.

      Text reports now also available in LaTeX format.

      Python 2.5 now supported.

      Fixed bug in reading genes annotations in GFF and NCBI formats.

      QUAST now can be rerun on existing Nucmer alignments files.


1.1   Mismatches counting.

      Fixed bug in misassemblies counting (some inversions were omitted).

      GC content plot is logarithmically scaled.

      ORFs are not counted, GeneMark added instead (for gene finding, only on Linux).

      Nucmer aligner setting changed (from IDY% = 80 to 95,
      i.e. now all alignments are more robust).


1.0   Initial open source release!
