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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkages but instead on whole genome alignments.
This issue is for tracking progress on the ribbon module in preparation for merging it into the main project.
Modify LASTZ wrapper to do pairwise alignments between a defined set of contigs
Add filter for alignment length and quality
Convert LASTZ output to .bed and .blocks files with wga2ribbon app
Extend wga2ribbon to use Minimap2 asm2asm alignment format
Hello Adamataranto,
have you managed to modify the synteny module to plot arbitrary alignments? Can you point me to a bioinformatic package that is able to do so? I'm currently searching for it but with no luck.
Thank you.
Hi Adamtarando,
thank you for the quick response. I'll try to explain what I want to do and what I can currently do with the data I have. I have two mitochondrial genomes of which I want to analyze the collinearity. However, I have yet to find a tool that allows for the analysis of non-coding regions. Currently I have the .bed files, .gff, .fasta and .blast of both mitochondrial genomes.
Thank you again for your help.
jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkages but instead on whole genome alignments.
This issue is for tracking progress on the ribbon module in preparation for merging it into the main project.
.bed
and.blocks
files with wga2ribbon appThe text was updated successfully, but these errors were encountered: