Comments (2)
Dijkstra's algorithm with edge weights given by the sequence length works well:
https://github.com/johnlees/unitig-counter/blob/master/unitig-graph/node_dists.cpp
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I think this is best left to pyseer/spydrpick as unitigs are likely to be better suited to this.
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Related Issues (20)
- What does "~~~" mean in the gene_presence_absence.csv file? HOT 1
- Re turned non-zero exit status 1. HOT 10
- Discrepancy in Gene Counts between summary_statistics.txt, pan_genome_reference.fa, and gene_presence_absence.csv HOT 4
- presence absence grid question HOT 3
- Clustering id confirmation HOT 2
- ERROR when writing output: double free or corruption (!prev): 0x000055f18142deb0 HOT 2
- Parallize pre-processing HOT 1
- cd-hit error in first run of Panaroo HOT 1
- Distinction between gene cluster names separated by "~~~" and "group_##". HOT 2
- Some problem about panaroo's result HOT 6
- A limit in number of input files? HOT 2
- gene presence/absence file having ";" without merging paralogs HOT 3
- Failure of `panaroo-merge` with `-a core` HOT 3
- error reading bakta gff3 files, conversion to prokka gff to make it working with panaroo 1.3.0 HOT 3
- RuntimeError: Error reading prokka input! HOT 4
- Interpretation of Gene Names and Downstream Analysis in Panaroo Pan-genome Studies HOT 1
- Refound Genes Exhibit In-Frame Stops and Frameshifts: Seeking User-Friendly Controls and Improved Understanding for Downstream Analysis HOT 7
- Error after while processing paralogs? HOT 7
- List text file input method not working HOT 6
- clustered_proteins file in output? HOT 1
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