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Utilize PHRED-scores for error removal, add 3D json compatibility#40

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evolp merged 44 commits into
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May 4, 2026
Merged

Utilize PHRED-scores for error removal, add 3D json compatibility#40
evolp merged 44 commits into
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@evolp evolp commented Mar 20, 2026 •
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Utilize PHRED-scores for error removal

  • the quality scores from the sequencing reads can be stored in a Reads
  • the scores are binned into four categories in accordance with this document on Illumina NovaSeq Quality Scores.
  • it can be used to assess the validity of each k-mer during graph construction
    • option 1: only include k-mers which have occurred with all bases having at least a specific quality
    • option 2: only include edges of k-mer occurrences with all bases having at least a specific quality, unless this would disconnect the k-mer on one or both sides
  • the quality scores can also be saved in the graph nodes by using the SummaryData implementations IDMapEMQualityData,SumMapEMQualityData, or TagsCountsPEMQualityData - this can be used to apply two error removal algorithms to the graph
    • DebruijnGraph::remove_lq_ladders_tips will remove any ladders (bubbles) and tips which are not supported by good quality k-mers.
    • DebruijnGraph::remove_lq_splits is more radical and will identify nodes at which the path splits into a good and bad quality path, or at which a good and bad quality path merge, and remove the connection to the bad quality path

3D JSON compatibility

  • a DebruijnGraph can now be saved to a JSON file compatible with https://github.com/vasturiano/3d-force-graph
  • default functions for node and edge format, which include all node information, are available: Node::node_json_default and Node::edge_json_default

evolp added 30 commits February 19, 2026 19:15
@evolp
add quality to reads
0d12325
@evolp
add quality summerizer, add qualty tracking to filter_kemers, add sim…
5bee532 
…ple quality based ladder removal
@evolp
fix print quality
b8553d6
@evolp
add path removal
8942d87
@evolp
update quality based ladder algorithm and add test
fd7f8d1
@evolp
switch high q path choice to best nb
7d741e3
@evolp
remove filter high q path choice
7ee2fb1
@evolp
remove filter low q path choice
40e2d67
@evolp
add tip removal
137715b
@evolp
add assert to test, rename function, remove print statements
df9f5da
@evolp
add remove_lq_splits
62199b1
@evolp
add validation to all summarizers except for group/rel count
ea403df
@evolp
make BaseQuality clap::ValueEnum
7cfceb7
@evolp
add warn message lq path removal
335c480
@evolp
modify warn message lq path removal
94aca58
@evolp
remove path length limit, fix tests
4d16e74
@evolp
add weights to dot edges
5063984
@evolp
add DebruijnGraph::to_json_3d
18257e7
@evolp
fix target node dir
d300dff
@evolp
fix quotation marks
8bcf0a5
@evolp
fix commas after edges
1c68b14
@evolp
fix ids space, fix commas in last entry
eda7cc7
@evolp
change quality json format to numerical
662e54b
@evolp
fix last partial node vec index
7cb9fc7
@evolp
add high max path limit for high path
ed50f15
@evolp
add max path limit bad q path, rm error path removal
8ff6a07
@evolp
add max bubble path len as argument
f7555ff
@evolp
remove serialized test graph from tests
1537bdc
@evolp
change json edge property value to strength
c2173a7
@evolp
Merge pull request #39 from jlab/feat/to-3d-json
9534973 
Feat/to 3d json

- add `DebruijnGraph::to_json_3d` and node and edge default formatting methods
- remove necessity for serialized test graphs in tests
@evolp evolp requested review from sjanssen2 and tensulin March 20, 2026 12:33
@evolp evolp linked an issue Mar 20, 2026 that may be closed by this pull request
Move test graph generation to this crate #38
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tensulin
tensulin approved these changes Apr 29, 2026
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@evolp evolp merged commit 32f2ffd into master May 4, 2026
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@tensulin tensulin tensulin approved these changes

@sjanssen2 sjanssen2 Awaiting requested review from sjanssen2

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Move test graph generation to this crate

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