PombertLab/SYNY: 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.