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Circos plot for contig–contig links supported by PacBio read alignments

I’m aligning PacBio long reads to a draft assembly and want a Circos plot showing contig–contig links supported by single reads (assembly QC, not scaffolding). Should links be built from primary only, primary + supplementary, or include secondary alignments? Any recommended tools or workflows for this visualization are welcome.

pacbio circos
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updated by Ram Ram • written by matvergara19 • matvergara19

Do you need to search/extract or just visualize reads that map to two different contigs?

If you want to visualize then JBrowse2 may be an alternate solution. See the various examples in the gallery: https://jbrowse.org/jb2/gallery/ Specifically this view : https://jbrowse.org/code/jb2/latest/?config=test_data%2Fconfig_demo.json&session=local-p8Awt4xmpe79gaSFK0hou

If you need to extract reads that are mapping to two different contigs then perhaps Fetch pairs of discordantly aligned reads or Get discordant read pairs from bam would be useful.

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written by GenoMax GenoMax

Thank you very much. I was able to extract the split reads, but now I'm trying to analyze whether one end of a contig overlaps with the other end of the contig, forming a scfold, all with a single read.

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written by matvergara19 • matvergara19

1 answer

Hey if u r trying to create circular map> instead of circos u can use CGview/Proksee server u just need to upload your .gbk file after annotation of your genome ..usefull if your genome is bacterial genome

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written by Abhijit • Abhijit

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