Table 3 Tools for pangenome graph-based genotyping and novel variant calling
From: Plant graph-based pangenomics: techniques, applications, and challenges
Tools | Methods | Calling | Genotyping | References |
|---|---|---|---|---|
Paragraph | Read mapping | – | SNP, indel, SV | Chen et al. (2019) |
Seven Bridges | Read mapping | – | SNP, indel, SV | Rakocevic et al. (2019) |
HISAT-genotype | Read mapping | – | SNP, indel | Kim et al. (2019) |
GraphTyper2 | Read mapping | SNP, indel | SNP, indel, SV | Eggertsson et al. (2019) |
vg | Read mapping | SNP, indel, SV | SNP, indel, SV | Hickey et al. (2020) |
Gramtools | Read mapping | – | SNP, indel, SV | Letcher et al. (2021) |
Minos | Read mapping | – | SNP, indel | Hunt et al. (2022) |
BayesTyper | k-mers comparisons | – | SNP, indel, SV | Sibbesen et al. (2018) |
PanGenie | k-mers comparisons | – | SNP, indel, SV | Ebler et al. (2022) |
KAGE | k-mers comparisons | – | SNP, indel | Grytten et al. (2022) |
EVG | k-mers and mapping | – | SNP, indel, SV | Du et al. (2024) |