SYNY-v1.2

Bugfix release

• Fixed concatenation issue with isoforms in list_maker.pl
• Fixed subranges issues in list_maker.pl
• Adjusted linearmap alpha value and edge color for readability in linear_maps.py
• Slightly reduced memory usage with matplotlib

SYNY-v1.1b

Bugfix release

• Fixed extra length issues with barplots, dotplots and linemaps. Code was missing a line.strip(). Issue created visual artefacts on barplots (longer frames).

Code cleanup:

• Added --version option for all scripts.
• Minor code cleanup / standardisation across scripts

SYNY-v1.1a

Changes

Additions

• Added the --include option to select contigs by name from text file(s); one name per line
• Added the --ranges option to select contig subranges from text file(s); name start end
• Added the --bpmode option to generate pairwise (pair) and/or concatenated (cat) barplots. Possible values are pair (default), cat, and all (for both).
• Added the --bclusters option to color clusters by alternating colors in the barplots. The colors are not related within or between contigs, they are just used to highlight collinear chunks.
• Created check_versions.pl to summarize script versions; this information can now be displayed with run_syny.pl --version.

Bugfixes

• list_maker.pl now grabs GeneID tags if locus tags are absent from GBFF annotation files.
• Fixed .txt file extension + added a file size check to paf_metrics.py. Now skips plotting if file is empty.
• Fixed div by zero issue in nucleotide_biases.pl.
• Added a check to detect if annotations parsed are blank. run_syny.pl no longer crashes if annotations are blank when running gene cluster inferences. If blank, it now now skips this section automatically.
• Fixed perl env shebangs causing issues with conda
• Fixed wrong exit codes with readmes

Readme / logs

• Added section about memory usage with genome alignments
• Added mashmap barplot examples in the Encephalitozoon section
• Added changes.md summarizing changes between versions
• Improved syny.log file.

SYNY-v1.1

Additions:

• SYNY now generates linear maps (aka linemaps) from PAF files with linear_maps.py.
• Added support for MashMap3 genome alignments. Mashmap can be selected instead of minimap with --aligner mashmap. It runs in a smaller memory footprint than minimap (if using its default percentage identity of 85%). It does not product exact alignments however.
• Added the option to exclude contigs by name matching regular expression(s): e.g. --exclude '^AUX' '^CPGT'.
• Added an alternate SYNY installation method that does not require sudo privileges by leveraging conda packages.

Fixes:

• Fixed the The number of annotation files (2) does not equal the number of protein files (1) error => rewrote the corresponding segment and removed the obsoleted subroutine.
• Fixed the unreliable $diamond_check in get_homology.pl (i.e. replaced which by command -v).
• Changed Perl dependency Roman => Text::Roman in nucleotide_biases.pl.

SYNY-v1.1

Changes:

Additions:

• SYNY now generates linear maps (aka linemaps) from PAF files with linear_maps.py.
• Added support for MashMap3 genome alignments. Mashmap can be selected instead of minimap with --aligner mashmap. It runs in a smaller memory footprint than minimap (if using its default percentage identity of 85%). It does not product exact alignments however.
• Added the option to exclude contigs by name matching regular expression(s): e.g. --exclude '^AUX' '^CPGT'.
• Added an alternate SYNY installation method that does not require sudo privileges by leveraging conda packages.

Fixes:

• Fixed the The number of annotation files (2) does not equal the number of protein files (1) error => rewrote the corresponding segment and removed the obsoleted subroutine.
• Fixed the unreliable $diamond_check in get_homology.pl (i.e. replaced which by command -v).
• Changed Perl dependency Roman => Text::Roman in nucleotide_biases.pl.

SYNY-v1.0b

Changes:

• run_syny.pl options can now be set from a configuration file (requires Getopt::ArgvFile); e.g. run_syny.pl @commands.conf
• Added the Getopt::ArgvFile dependency to setup_syny.pl => sudo cpanm Getopt::ArgvFile
• Added a minimum contig size option + set defaults to all contigs, i.e. (--minsize 1)
• Added a matplotlib color palette check before computations so that plots won't crash if the color palette entered does not exist

SYNY-v1.0a

Changes:

• Added --hfsize , --hmin, --hmax and --hauto options to heatmaps
• Added more options to the Circos --labels command line switch. Possible values are now: mixed, roman, arabic and names
• Added --pthreads option to set the limit of plotting instances to run in parallel (in case each plot eats up too much RAM); defaults to the value set by --threads if omitted.
• Added SVG output to paf_metrics.py
• Set fonts as editable in SVG output files
• Removed unnecessary border frames from barplots
• Fixed ambiguous heatmap titles
• Added an example script (Arabidopsis.sh) in Examples/ to download two Arabidopsis genomes (~ 100-150 Mbp each) for testing purposes

SYNY-v1.0

Stable release

Changes:

Misc:

• Fixed output directory bug in run_syny.pl when using a deep tree
• Fixed abs_path() issue in setup_syny.pl that caused incomplete paths in the output configuration file
• Created check_mp_colors.py to list/plot color palettes available on the system (Fedora 40/Ubuntu 22.04 matplotlib palettes are not the same - 170 vs. 166) + added color palette plot
  (Images/python_color_palettes.png)
• Fixed out of bounds barplot legends
• Added font size options --bfsize/--dfsize options for barplots/dotplots

Circos:

• Contigs from the reference genome are now visually distinct and are labelled by roman numerals. Other contigs are labelled by arabic numerals.
• Added --orientation option (possible values: normal, inverted, both) + removed the now obsoleted --no_invert/--no_normal options
• Added --no_cticks option to disable ticks in Circos plots.
• added --no_ntbiases option to disable nucleotide bias subplots.
• Changed the default Circos plot mode to pairwise (--circos pair); concatenated plots can take a while to compute and are not always useful.
• Circos figures are now plotted in --orientation normal by default instead of both normal/inverted => less wasteful.
• Renamed the .genotype files generated by SYNY as .karyotype to match the nomenclature used by Circos

SYNY-v0.9e

Cleanup release:

• Fixed a bug that crashed nucleotide_biases.pl when the reference entered was not found. Now uses the first sequence alphabetically if the ref entered is not found.
• Created fasta_to_gbff.pl to convert FASTA sequences to GBFF files (without annotations); useful to compare newly assembled genomes using pairwise alignments
• Added Alignments, Clusters, Plots, and Utils subdirs to the git repository and moved scripts/data accordingly
• Added shell scripts to download the example annotation data from NCBI
• Improved/cleaned up README

SYNY-v0.9d

Cleanup release:

• Sanitized output directory:
  • Regrouped subdirs by analysis (ALIGNMENTS/, CLUSTERS/) and moved content accordingly
  • Created PLOTS/ subdir and moved all plots therein
  • Renamed the CIRCOS data folder as CIRCOS_DATA/ for greater clarity
  • Created SEQUENCES/ subdir to store genome and protein fasta files
• Restructured/cleaned up run_syny.pl
• Improved the output log (syny.log)

SYNY-v0.9c

• Simplified default help message
• Added --help option => displays all command lines options
• Added --no_clus option => turns off gene cluster inferences
• Added --no_circos, no_barplot and no_heatmap options => skips the correspoding plots
• Now generates both pairwise and concatenated Circos plots; --circos all is set as default