Collect speed results, sim accuracy results, and real calling results for Giraffe all together - Githubissues

vgteam / long-read-giraffe-experiments

Experimental materials for testing the long-read mapping abilities of vg giraffe

Other

4 stars 0 forks source link

Collect speed results, sim accuracy results, and real calling results for Giraffe all together #54

Open adamnovak opened 2 months ago

adamnovak commented 2 months ago

Might want to attach WDL running to the SnakeMake to fill in the calling results automatically.

Statistics:

Mapping speed
Softclipped and unmapped bases
Simulated mapping accuracy
Variant calling accuracy

Conditions:

Mapping to HPRC M/C graph with Giraffe (minimum condition for all techs to say "it works" and fix a version)
- Might need to add next pangenome release in before paper comes out
Mapping to linear stick graph with Giraffe
Mapping to 64-haplotype downsampled 1KG graph from original Giraffe paper
Mapping to linear reference with Minimap2 (but also BWA-MEM for Illumina)
Maybe mapping to a more collapsed graph as an internal metric

Read Sets:

HiFi
R10
Illumina (paired end) (non-chaining codepath) (haplotype sampling mode only)
- Lets us say we have one mapper for long and short reads even though it's a different codepath, "universal mapper"

Could be a big Google Sheets.