commands.conf

### Example of a run_syny.pl configuration file
### Edit / comment out/ comment in options as desired

################################################################################
### General options
################################################################################

### GenBank GBF/GBFF Annotation files (GZIP files are supported)
# --annot *.gbff.gz

### Output directory [Default = SYNY]
--outdir ./SYNY

### Number of threads to use [Default: 16]
--threads 16

### Number of graphs to plot in parralel; defaults to --threads if unspecified
# --pthreads 8

### DIAMOND BLASTP evalue cutoff [Default = 1e-10]
--evalue 1e-10

### Allowable number of gaps between gene pairs,e.g. --gaps 0, 1, 5 [Default = 0]
--gaps 0

### Minimum contig size (in bp) [Default: 1]; i.e. investigates all contigs
--minsize 1

### Select contigs with names from input text file(s) (one name per line); i.e. exclude everything else
# --include names.txt

### Select contigs with subranges from input text file(s): name start end
# --ranges ranges.txt

### Exclude contigs with names matching the regular expression(s); e.g. --exclude 
# --exclude '^AUX'

### Specify genome alignment tool: minimap or mashmap [Default: minimap]
--aligner minimap

### Specify minimap2 max divergence preset (--asm 5, 10 or 20) [Default: off]
# --asm 20

### Specify mashmap percentage identity [Default: 85]
--mpid 85

### Resume minimap2 computations (skip completed alignments)
# --resume

### Skip minimap2 pairwise genome alignments
### --no_map

### Skip minimap VCF file creation (files can be quite large)
### --no_vcf

### Skip gene cluster reconstructions
# --no_clus

################################################################################
### Plotting options
################################################################################

##########################################
# Circos
##########################################

### Circos plot mode: pair (pairwise), cat (concatenated), all (cat + pair) [Default: pair]
--circos pair

### Karyotype orientation: normal, inverted or both [Default: normal]
--orientation normal

### Prefix for concatenated plots [Default: circos]
--circos_prefix circos

### Reference to use for concatenated plots; uses first genome (alphabetically) if ommitted
# --ref reference_name

### Size unit (Kb or Mb) [Default: Mb]
--unit Mb

### Sliding windows size (nucleotide biases) [Default: 10000]
--winsize 10000

### Sliding windows step (nucleotide biases) [Default: 5000]
--stepsize 5000

### Contig label type: mixed (arabic + roman numbers), arabic, roman, or names [Default: mixed]
--labels mixed

### Contig label size [Default: 36]
--label_size 36

### Contig label font [Default: bold]. Possible fonts are: light, normal, default, semibold, bold, italic, bolditalic, italicbold
--label_font bold

### Set max number of ticks [Default: 5000]
--max_ticks 5000

### Set max number of ideograms [Default: 200]
--max_ideograms 200

### Set max number of links [Default: 75000]
--max_links 75000

### Set max number of points per track [Default: 75000]
--max_points_per_track 75000

### Load custom colors from file
# --custom_file custom_color_2.txt

### List available custom color presets
# --list_preset

### Use a custom color preset, e.g.: --custom_preset chloropicon
# --custom_preset chloropicon

### Color by cluster instead of contig/chromosome [Default: off]
# --clusters

### Turn off nucleotide biases subplots
# --no_ntbiases

###  Turn off GC / AT skews subplots
# --no_skews

### Turn off ticks in Circos plots
# --no_cticks

### Turn off Circos plots
# --no_circos

##########################################
# Barplots
##########################################

### Barplot figure height in inches [Default: 10.8]
--bheight 10.8

### Barplot figure width in inches [Default: 19.2]
--bwidth 19.2

### Barplot font size [Default: 8]
--bfsize 8

### Barplot color palette [Default: Spectral]
--palette Spectral

### Use a monochrome barplot color instead: e.g. --monobar blue
# --monobar blue

### Color by cluster alternating colors; colors are not related within/between contigs; [Default: off]
# --bclusters

### Barplot mode: pair (pairwise), cat (concatenated), all (cat + pair) [Default: pair]
--bpmode pair

### Turn off barplots
# --no_barplot

##########################################
# Dotplots
##########################################

### Dotplot figure height in inches [Default: 10.8]
--dheight 10.8

### Dotplot figure width in inches [Default: 19.2]
--dwidth 19.2

### Dotplot font size [Default: 8]
--dfsize 8

### Axes units multiplier (for dotplots) [Default: 1e5]
--multi 1e5

### Dotplot color [Default: blue]
--color blue

### Horizontal distance (width) between subplots [Default: 0.05]
--wdis 0.05

### Vertical distance (height) between subplots [Default: 0.1]
--hdis 0.1

### Use a color palette instead: e.g. --dotpalette inferno
# --dotpalette inferno

### Turn off ticks on x and y axes
# --noticks

### Turn off dotplots
# --no_dotplot

##########################################
# Heatmaps
##########################################

### Heatmap figure height in inches [Default: 10]
--hheight 10

### Heatmap figure width in inches [Default: 10]
--hwidth 10

### Heatmap font size [Default: 8]
--hfsize 8

### Heatmap color palette [Default: winter_r]
--hmpalette winter_r

### Set maximum color bar value [Default: 100]
--hmax 100

### Set minimum color bar value [Default: 0]
--hmin 0

### Set color bar values automatically instead
# --hauto

### Turn off heatmaps
# --no_heatmap

##########################################
# Linemaps
##########################################

### Linear map figure height in inches [Default: 5]
--lheight 5

### Heatmap figure width in inches [Default: 20]
--lwidth 20

### Reference genome color palette [Default: Spectral]
--lm_rpalette Spectral

### Target genome color palette [Default: Blues]
--lm_xpalette Blues

### Contig name rotation [Default: 90]
--lmrotation 90

### Font size [Default: 8]
--lfsize 8

### Turn off linemaps
# --no_linemap