Table 4 URL, version, pangenome representation, and parameters of the three analyzed tools. pggb/0.2.0 used wfmash v0.7.0, seqwish v0.7.3, and smoothxg v0.6.1
From: Comparing methods for constructing and representing human pangenome graphs
Tool | Github repository | Graph type | Version | Parameters |
|---|---|---|---|---|
Bifrost | pmelsted/Bifrost | De Bruijn graph | 1.0.5 | -k100 -c |
pggb | pangenome/pggb | variation graph | 0.2.0 | -p 98 -s 10000 -k 311 -G 13033,13117 |
-O 0.03 -v -t 8 -T 8 -A -Z | ||||
Minigraph | lh3/Minigraph | variation graph | 0.18 | -cxggs |
Minigraph-Cactus | ComparativeGenomics | variation graph | 2.2.3 | –maxLen 10000 –delFilter 10000000 |
Toolkit/cactus | ||||
mdbg | ekimb/rust-mdbg | De Bruijn graph | 1.0.1 | -k 10 -d 0.0001 –minabund 1 –reference |