Table 1 Comparison of four construction methods of pangenome
Feature | Iterative mapping and assembly | Map-to-pan | De novo assembly | Graph pangenome |
|---|---|---|---|---|
Reference | Reference-based | Reference-based | Reference-free | Reference-free |
Assembly level | Short reads | Contigs | Genomes | Genomes |
Alignment approach | Iterative alignment | Genome-wide alignment | ||
Sequencing depth requirements | Low depth | Low depth | High depth | High depth |
Scope of application | Large-scale group | Large-scale group | Few individuals | Few individuals |
Sequence storage | Liner | Liner | Liner | Graphic entity |
Computing resource requirements | Low | Large genomes are in high demand | Higher | Higher |
Analysis of SVs | Only SNPS and indels can be identified | Interindividual CNVs | Large SVs | Some highly divergent SVs |
Cost | Low | Medium | Higher | Higher |
Limitation | The sequence fragment is too short to analyze CNV | Not suitable for scale analysis of complex genomes | The genome needs to be annotated, which would lead to bias | Visualizing storage is difficult and ambiguity may arise during sequence alignment |