SYNY-v1.3.2

Bugfix release

• list_maker.pl: Fixed an issue arising from LOCUS and ACCESSION tags being different in NCBI GBFF files, e.g.:
  LOCUS JBLUPJ010000002
  ACCESSION JBLUPJ010000002 JBLUPJ010000000
  list_maker.pl now looks for the ACCESSION base (located to the right) and comprehensively reassigns the missing NCBI accessions.
• gff3_to_gbff.pl: Fixed an issue where transcript entries in GBFF files were improperly reassigned as mRNA; this reassignment was intended only for AGAT GBFF files.
• gff3_to_gbff.pl and fasta_to_gbff.pl: Added a fix for single contigs/chromosomes >= 1 Gbp.

SYNY-v1.3.1

Bugfix release

• paf_to_barplot.py, paf_to_dotplot.py, linear_maps.py: Added a try/except block to prevent (rare) multiprocessing pool crashes; if exceptions are detected, plots will be generated using a single-threaded for loop instead.

SYNY-v1.3.0

Changes

• Changed versioning to PEP 440
• run_syny.pl: Added the --min_asizecommand line option to filter out alignments/clusters smaller than integer value (e.g. --min_asize 5000)
• run_syny.pl: get_paf.pl, paf_metrics.py: Added the --no_sec command line option to filter out secondary alignments from minimap2 alignments.
• gff3_to_gbff.pl:
  • Annotations in the GFF3 files are now sorted by start positions => annots in GFF3 files can be out-of-order
  • Fixed a bug that crashed the script when dealing with contigs without annotations.
  • Added preliminary support for AGAT-converted files (tested on a few user-provided files).
  • Added the --id command line option to label products by ID tags. Can be useful with GFF3 files that do not contain product descriptions.
• jgi_to_ncbi_gff.pl: New script that converts JGI GFF files to a NCBI-like GFF3 format compatible with gff3_to_gbff.pl.
• list_maker.pl: If locus_tags and GeneID tags are missing from GBFF files, now checks for gene tags and assign automatic locus_tags.
• get_synteny.pl: Fixed a bug with median calculations if # of values < 2.

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