sourmash taxonomy visualization brainstorm
Relevant Issues/PRs:
- sourmash-bio/sourmash#1515
- sourmash-bio/sourmash#969
- sourmash-bio/sourmash#1011 (comment)
- sourmash-bio/sourmash#985 (comment)
- sourmash-bio/sourmash#1543
Relevant Repos:
- https://github.com/dib-lab/2018-ncbi-lineages
- https://github.com/dib-lab/sourmash_databases
- https://github.com/dib-lab/2019-12-12-sourmash_viz
- https://github.com/luizirber/2020-cami
- sourmash-bio/databases#11 <- build databases from assembly_stats.txt
/home/irber/sourmash_databases/outputs/lca/lineages
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plots that should be acheivable from sourmash gather results
krona taxonomy plot
- publication: https://link.springer.com/article/10.1186/1471-2105-12-385
- language: javascript, perl
- execution environment: bash
- github: https://github.com/marbl/Krona
- required input: text file
BURRITO interactive plot
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BioSankey
- publication: https://www.degruyter.com/document/doi/10.1515/jib-2017-0063/html
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Biosankey (left)
Biosankey for change over time
MetaCoder
- publication: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404
- language: R
- execution environment: R
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Heatmap
- summary:
- publication: NA; this particular heatmap is from MetaPhiAn but we could make our own
- language: python, R
- execution environment: python, R
- github: NA
- required input:
KEANU
- summary: acheives the same style as other graphics, but in pure python. Could be good inspiration for viz notebooks?
- publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2629-4
- language: python
- execution environment: python
- github: https://github.com/IGBB/keanu
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plots that require substantially more compute or metadata etc.
co-occurence of species in a group of metagenomes
- summary: co-occurence would need to be calculated from gather-species level summaries...probably.
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Iroki
- publication: https://www.iroki.net/wiki
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