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saramarti2.bsky.social
•
95 days ago
Gemma, we are interested in visualizing the alignment between two plasmids in a circular format. Could you recommend us a tool?
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[–]
martinsteinegger.bsky.social
•
93 days ago
Maybe Anvio from @merenbey.bsky.social can do this
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celiasouque.bsky.social
•
93 days ago
For circular plots, I have found that out of the box elderly BRIG
https://beatsonlab.com/softwares/brig/
remains the best. Otherwise for more custom plots I usually go with circos-like packages (like pyCirclize in Python) but it is much more work
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zaminiqbal.bsky.social
•
93 days ago
Cc @celiasouque.bsky.social
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bradfordptaylor.bsky.social
•
93 days ago
Not the most visually appealing, but I’ve found dot plots (eg, via mummer/nucmer) adequate
Check out our preprint:
https://www.biorxiv.org/content/10.1101/2022.11.01.514792v1
Caveat, the results in the paper are underpowered because a lack of funding to sequence more. The figures are fine though
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gaworjan.bsky.social
•
93 days ago
https://github.com/moshi4/pyGenomeViz
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gemmaatkinson.bsky.social
•
93 days ago
Hi Sara, hm good question. I don’t think I’ve come across such a tool, but I’ll share your question
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saramarti2.bsky.social
•
93 days ago
thanks!!!
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saramarti2.bsky.social
•
93 days ago
Thanks everyone for your help!!! ☺️
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joaoftsbotelho.bsky.social
•
93 days ago
Maybe proksee will help? Or BRIG
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Check out our preprint: https://www.biorxiv.org/content/10.1101/2022.11.01.514792v1
Caveat, the results in the paper are underpowered because a lack of funding to sequence more. The figures are fine though