SYNY-v1.2a

Changes

• Now generates VCF files from minimap2 genome alignments (min. alignment length = 1000 bp) automatically. VCF file creation can be turned off with the new --no_vcf flag in run_syny.pl (and/or in get_paf.pl). Note that these files can become quite large depending on the size of the genomes being compared.

• nucleotide_biases.pl now calculates GC and AT skews. Corresponding data files are located in the PLOTS/CIRCOS_DATA/ subdirectory.

• GC/AT skews are now plotted automatically with Circos. If desired, these subplots can be turned off independently with the --no_skews option, or together with all nucleotide biases subplots (with --no_ntbiases).

• Added a simple Fasta + GFF3 to GBFF converter (gff3_to_gbff.pl) in the Utils/ subdirectory. This tool was tested on NCBI GFF3 files and expects the GFF3 file(s) to include gene/mRNA/exon/CDS entries in the type column and the ID and Parent tags in the attributes column. It also expects the corresponding Fasta and GFF3 files to share the same prefixes (e.g. genome_1.fasta / genome_1.gff). The GBFF files thus created were designed to work with SYNY but do not adhere exactly to the GBFF format and may not work for other purposes.

• list_maker.pl/ run_syny.pl: GenBank Flat file format extensions (gbk, gb, gbf) are now recognized/accepted

• check_mp_colors.py: removed obsolete references to pylab

• Added orient_fastas_to_reference.py to the Utils/ subdirectory. This script reorients contigs in FASTA file(s) based on BLASTN homology searches against a reference. This can be useful when working with newly assembled genomes.

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)