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sourmash plugins - ideas dumping ground #2453

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ctb opened this issue Jan 31, 2023 · 11 comments
Open

sourmash plugins - ideas dumping ground #2453

ctb opened this issue Jan 31, 2023 · 11 comments

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@ctb
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ctb commented Jan 31, 2023

ref #1353

@ctb
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ctb commented Jul 25, 2023

Venn diagrams!

https://github.com/sourmash-bio/sourmash_plugin_venn

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ctb commented Jul 31, 2023

import and export functionality for sketches and signatures to CSV, etc.

taxonomy format loading, including via URLs; greengenes per #2538. support mechanisms discussed in #2694

cluster and cocluster a la #700
uniqify script #1265
dendrogram clustering/cut code a la #459

kSpider directly :)

more hash manipulation approaches per #1266
especially import/export #1098
contig manipulation per #1266 (comment)

upsetr plots per #1098 (comment)

mastiff CLI search as plugin @bluegenes
metadata manipulation stuff for mastiff

improved sourmash compare plotting #2587 including maybe PCoA style stuff
update: see the betterplot plugin

@ctb
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ctb commented Jul 31, 2023

could be kind of cool to support within-sample/between-sample metagenome distance display a la Amy Willis suggestion. @hehouts will no doubt be on it :)

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ctb commented Jul 31, 2023

picklist plugins! It would be nice to allow more complex picklist-style actions. maybe even via taxonomy or non-standard metadata.

@ctb
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ctb commented Aug 2, 2023

search upgrade as a plugin? see: #2002

@ctb
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ctb commented Aug 2, 2023

sketchall (fixing part of #2458) is in progress over at https://github.com/sourmash-bio/sourmash_plugin_sketchall

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ctb commented Aug 5, 2023

@ctb
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ctb commented Aug 17, 2023

making database covers... ref #1852 (comment)

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ctb commented Aug 17, 2023

database auto download support - there's an issue on this somewhere...

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ctb commented Aug 19, 2023

could make multigather a plugin? ref #1614

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ctb commented Jan 9, 2024

use a plugin to support the multifile sketch stuff that I implenented in sourmash-slainte! viz dib-lab/sourmash-slainte#7, and maybe dib-lab/sourmash-slainte#11

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