This has the potential to be misinterpreted due to I, II, III. Instead, give an example genome assembly file.
# this file is called config.yaml
ignore_autobreaks: True # Skip steps to find breaks in synteny blocks
diamond_or_blastp: "diamond" # "diamond" or "blastp"
plot_LGs: True # Plot the ALGs based on the installed databases
plot_sp_sp: True # Plot the synteny between two species, if False just generates .rbh files
species:
Celegans:
proteins: /path/to/proteins_in_Cel_genome.fasta # required field
chrom: /path/to/Cel_annot.chrom # required field
genome: /path/to/Cel_genome_assembly.fasta # required field
genus: "Caenorhabditis" # This is an optional field
species: "elegans" # This is an optional field
minscafsize: 1000000 # optional field. Sets minimum scaffold size to plot.
manual_breaks: # optional field, tells the software to treat breaks
- "I:50000" # as separate units for calculating the homology p-values
- "IV:9000000" # with Fisher's exact test. Useful for plotting centromeres.
- "II:99009" # Here, we tell the software that Cel chroms I, IV, II have breaks.
plotorder: # This optional field tells the software to only plot the scaffolds
- "I" # listed here, and to do it in this order. This is useful for plotting
- "II" # comparisons between two species where you want a specific order for
- "III" # both species.
Homosapiens:
proteins: /path/to/Human_prots.fasta
chrom: /path/to/Human_annotation.chrom
genome: /path/to/Human_genome_assembly.fasta
This has the potential to be misinterpreted due to I, II, III. Instead, give an example genome assembly file.