Quast

1. Fixed relatively rare bug of BSS when using large --min-alignment.

2. Improved check of previously generated results before reusing them.

3. GeneMark licence files are updated.

1. Fixes in pip installation:
- ignoring bdist_wheel and running regular installation instead;
- no installation of aux files (LICENSE, Manual, etc);
- proper error message about missing test_data dir (if "--test" is used).

2. Fixed conda installation (no GeneMark installation if there is no home dir)

1. Switch from major.minor to major.minor.patch versioning.

2. Python 3.6 is now supported (and all future Python 3.* versions).

3. Best set selection algorithm is significantly sped up.

4. GeneMark licence files are updated; expired licence error message is better
handled now.

5. Support email address is updated.

6. Fixed several minor but nasty bugs.

- always visible and scrollable Contig Info panel;
- new color (dark green) for contigs without misassemblies but having at
least 50% of their length in unaligned fragments.

2. MetaQUAST updates:
- parallel reference processing;
- expandable "i/s translocations" and "possible mis. contigs" metrics on the
main HTML report;
- GC distribution plots for the combined reference;
- new option ("--use-input-ref-order") to use originally specified order of
the references in the summary plots (PDF/PNG/etc only);
- stop processing with error message if any of the provided references is
empty or has incorrect sequences (non-ACGTN characters or header-only).

3. New plots are added (in static PDF/PNG/etc and interactive HTML formats):
- Feature-Response Curve (FRCurve) for misassemblies (both formats)
and genes/operons (static PDF/PNG/etc only);
- Distribution of contigs with GC % in a certain range (both formats);
- MUMmer plot of assembly against reference mapping (static HTML only).

4. Contig coordinates of the provided genes/operons annotations are saved to
<output_dir>/genome_stats/<assembly_name>_genes.txt and _operons.txt.

5. Broken scaffold assemblies (see "--scaffolds" option) are now filtered based on
"--min-contig" value (default is 500 bp) similarly to regular assemblies processing.
"Total length >= N bp" and " contigs >= N bp" metrics are no more reported for
these assemblies if N is less than the min contig threshold.

6. In order to avoid confusion, "--meta" option was renamed to "--mgm" (MetaGeneMark).

7. Internal overlaps between adjacent aligned blocks of a misassembled contig are
always excluded. Previously the processing depended on "--ambiguity-usage" value.

8. Small change in the installation strategy: if quast_libs directory has no write
permission (e.g. after sudo setup.py install), external packages (e.g. SILVA 16S
database; Manta SV caller) are downloaded to ~/.quast/ on the first use.

9. Gnuplot version 5.0 is added to the installation package.

10. GeneMark license files are updated.

11. Fixed several minor bugs.

- buttons for expanding overlapped alignments are added to detailed assembly tracks
on Contig Alignment Viewers;
- additional colors (available in all viewers) for:
* ambiguous contigs,
* alternative blocks of misassembled contigs,
* misassembled contigs with >50% unaligned bases (see item 7 below).
- better performance on low resolution screens.

2. Python3 is now supported (versions 3.3, 3.4 and 3.5).

3. Several new options are added:
- "--scaffold-gap-max-size" for controlling maximum allowed size of scaffold gap
inconsistency in the corresponding type of misassembly (--scaffolds only);
- "--fragmented-max-indent" for controlling maximum allowed indent on each side
of the reference fragments to consider translocation as fake one (see manual for
details);
- "--blast-db" for specifying custom BLAST database instead of SILVA 16S rRNA for
searching probable references in MetaQUAST "without references" mode;
- "--space-efficient" for removing or even not creating space consuming auxiliary
files; all reports and plots (except Icarus viewers) are generated as usual;
- "--significant-part-size" renamed to "--unaligned-part-size", see details below
(see item 6 below).

4. New metric, report and plot are added (MetaQUAST only, combined reference only):
- possible misassemblies (number of putative interspecies translocations
in possibly misassembled contigs if each large unaligned fragment is supposed
to be a fragment of unknown reference);
- report of interspecies translocations number per each reference, saved to
interspecies_translocations_by_refs_<assembly_name>.info under
<output_dir>/combined_reference/contigs_reports/;
- plot of all found and supposed (possible) interspecies translocations, saved to
intergenomic_misassemblies.pdf under the same folder as above report.

5. New detailed report is added:
- all fully and partially unaligned contigs, their length, and unaligned parts are
listed in <output_dir>/contigs_reports/contigs_report_<assembly_name>.unaligned.info

6. Partially unaligned contigs are redefined in simpler and more logical way. Now
all contigs having at least one unaligned fragment of length greater or equal to
unaligned_part_threshold are considered as partially unaligned. The threshold is
controlled by --unaligned-part-size option (default value is 500 bp).

7. New processing of misassembled contigs which are mostly unaligned (> 50%):
- " half-unaligned with misassembly" metric is renamed to " unaligned mis. contigs"
and moved from detailed unaligned_report to detailed misassemblies_report
(stored under <output_dir>/contigs_reports/);
- " unaligned mis. contigs" metric is added to all main reports (TXT, HTML, PDF).

8. BED format is accepted for genes/operons annotations.

9. Minor changes in HTML reports:
- heatmap coloring is removed for metrics where best/worst values are undefined
(GC %, similar blocks, contigs, etc);
- split versions of scaffold assemblies are plotted with dashed lines (--scaffolds
option only).

10. Fixed issue of crashing E-MEM on OS X without gcc installed. Also, if E-MEM is
already installed on the system, it will be used instead of embedded E-MEM.

11. User-provided SAM/BAM files are now checked for correct chromosome names and
automatically corrected if needed and correction is possible.

12. Fixed incorrect behaviour of MetaQUAST on compressed assemblies in "without
references" mode.

13. Best set selection is improved (misassembly detection algorithm in case of multiple
ambiguous mappings of contig fragments). Now BSS takes internal overlaps into
account, so alignments with a short gap (in contig) are preferred over alignments
having large internal overlap if all other things are equal.

14. Fixed several minor bugs.

15. Icarus citation is updated.

16. Useful tips on running QUAST on large genome assemblies are added to FAQ section
of the manual (see Q14).

- predicted genes (see --gene-finding option) are now displayed in contigs (on both
Contig Size and Contig Alignment Viewers);
- zoom buttons added to read coverage panels insteads of log/normal scale switch;
- small fixes for better performance on low resolution screens.

2. setup.py is added for simplifying QUAST installation process.

3. Heavy output files (lists of SNPs, GFF with predicted genes) are now compressed
with gzip. This default behaviour may be cancelled by using --no-gzip option.

4. Automatic suggestion to use --scaffolds option if assembly contains long continuous
fragments of N's.

5. Embedded samtools is replaced with sambamba which is significantly faster.

6. Embedded bowtie2 is replaced with BWA-MEM which is more accurate.

7. E-MEM is also working under OS X now (in addition to Linux).

8. Removed limitation of not moving QUAST installation dir after the first use.

9. Fixed bug causing creation of error.log file in current working directory.

10. Fixed improper Duplication ratio calculation in some MetaQUAST runs.

11. Requests to NCBI are switched to HTTPS which will be mandatory after September 30, 2016.

12. SILVA database release is updated from 119 to 123 (it is downloaded on the first use).

13. Fixed several minor bugs.