JupiterPlot
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JustinChu
A Circos-based tool to visualize genome assembly consistency
Hello, I notice that I don't get similar results from ref=reference.fa fa=scaffolds.fa as I do with ref=scaffolds.fa fa=reference.fa. I am looking at one sequence in reference.fa, and 4 sequences in...
Hi there, I used the JupiterPlot to present the synteny between two genomes using default parameters: ./jupiter name=genome_two ref="polished_assembly.fa" fa="C_1.0_genomic.fna" t=32 ng=75 Attached is the circos plot generated. I wonder...
Hi, just tried this pipeline to see if I could visualize synteny between two chromosome level assemblies of quite closely related fish species. I was wondering about two things: Is...
Hi, I have been running JupiterPlot to compare an assembly to a reference genome and ended up with fractions of scaffolds (new assembly) aligning to the reference genome. However, the...
A very minor addition: when users set a maxScaff value, the coverage is variable based on overall length of those `maxScaff` scaffolds. This makes the code to output the resulting...
There is a minor compatibility issue regarding the `cp` command used. Changing the `-f` parameter location might be all that is needed.
Usually the output for this will be messy, but users should have the option of adding helpful labels in the plot
incongruent links would be outliers compared to the true position (chromosome position & distance from in link) of the link. This could be done to highlight where misassemblies occur.
When comparing assembles that are both fragmented, some reference seqeunces are likely not well ordered, leading to the appearance of incongurent linkts. It may be possible to iteratively place the...
I currently filter MAPQ < 50 and any alignments with an XA tag to minimize noise in the plot. These filtering options should be an option since things like repeat...