You need to run BUSCO on your genome assembly using the nematoda_odb10 dataset.
This script takes as input the resulting full_table.tsv.
You can now paint your genome by Nigons online. Simply upload your BUSCO full_table TSV file to https://pgonzale60.shinyapps.io/vis_alg/.
There are two variables that are important in the interpretation of the plot: the bin size and the minimum number of loci. These determine which, if any, scaffolds will be excluded from the plot. Small scaffolds are intentionally excluded as Nigons can only be meaningfully interpreted in multimegabase long sequences.
The bin size determines at which span the BUSCO loci will be grouped. However, it also filters out scaffolds whose loci at the most distant part is less than twice the bin size. For example, if using a bin size of 500,000, and the assembly contains a scaffold with many BUSCO loci, but all of them found in only the first 900,000 basepairs of the sequence, this scaffold would be excluded from the plot.
The other filtering parameter is the number of loci. This one simply excludes scaffolds that have less than x number of BUSCO loci.
The height and width parameters do not affect the online plot. These only affect the PDF that we recommend you to download. Adjust the width and height of the PDF plot to fit the size of your scaffolds.
We do not have access to the files you upload.
If you prefer to create the plot locally, I recommend to install the dependencies via conda and to do so in a new conda environment to avoid conflicts with other packages.
# Define name for new conda environment
ENV_NAME=vis_alg
# Create environment and install dependencies
conda create -n $ENV_NAME -c r -c conda-forge icu=58 r-dplyr=0.8 r-readr=1.3.1 r-scales=1.1.1 r-gtools=3.8.2 r-optparse=1.6.6 r-ggtext=0.1.0 xorg-libxrender=0.9.10 -y
# Activate conda environment
conda activate $ENV_NAMEThen get the script and the Nigon defintion found in this repository.
git clone https://github.com/pgonzale60/vis_ALG.git
cd vis_ALG/You will need to specify the result of BUSCO and the location of the Nigon element dictionary.
Rscript bin/vis_ALGs.R -b full_table.tsv -n data/gene2Nigon_busco20200927.tsv.gz -s Genus_species -o output.pngThere are two examples which you can use to test: Caenorhabditis elegans and Oscheius tipulae full_table.tsv resulting from BUSCO v4 using nematoda_odb10.
To generate a PNG image of the Nigon elements in O. tipulae chromosomes you can execute
Rscript bin/vis_ALGs.R -b examples/oscheius_tipulae.local.v3_1rx.full_table.tsv -n data/gene2Nigon_busco20200927.tsv.gz -s Oscheius_tipulae -o otipu.pngTo generate a JPEG image of the Nigon elements in C. elegans chromosomes you can execute
Rscript bin/vis_ALGs.R -b examples/oscheius_tipulae.local.v3_1rx.full_table.tsv -n data/gene2Nigon_busco20200927.tsv.gz -s Caenorhabditis_elegans -o cele.jpegExample PNG Oshceius tipulae Nigon painting:
-b FILE.TSV, --busco=FILE.TSV
busco full_table.tsv file
-n FILE.TSV, --nigon=FILE.TSV
busco id assignment to Nigons [default=gene2Nigon_busco20200927.tsv.gz]
-w INTEGER, --windowSize=INTEGER
window size to bin the busco genes [default=500000]. Sequences shorter than twice this integer will not be shown in the plot
-m INTEGER, --minimumGenesPerSequence=INTEGER
sequences (contigs/scaffolds) with less than this number of busco genes will not be shown in the plot [default=15]
-o FILE, --outPlot=FILE
output image [default=Nigons.jpeg]. Should include one of the following extensions: eps, ps, tex, pdf, jpeg, tiff, png, bmp or svg
--height=INTEGER
height of plot. Increase this value according to the number of ploted sequences [default=6]
--width=INTEGER
width of plot [default=5]
-s GENUS_SPECIES, --species=GENUS_SPECIES
Title to be italicized in the plot [default=]
-h, --help
Show this help message and exit
The nematoda ODB 10 loci assessed by BUSCO were classified into Nigons as described in Gonzalez de la Rosa, Pablo Manuel, et al. "A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes." G3 11.1 (2021): jkaa020.
