Table 3 The ten assembly approaches tested
Tool | Application | Abbreviation |
|---|---|---|
MegaHit | short read metagenome assembler | short read |
Redbean | long read genome assembler | long read |
Canu | long read genome assembler | long read |
metaFlye | long read metagenome assembler | long read |
Racon | polishing long read assemblies with long reads | long read |
HybridSpades | hybrid genome assembler; short read assembly followed by long read scaffolding | short read hybrid |
Opera-MS | hybrid metagenome assembler; short read assembly followed by long read scaffolding either (1) de novo or (2) using reference genomes | short read hybrid |
ntEdit | polishing long read assemblies with short reads | long read hybrid |
Pilon | polishing long read assemblies with short reads | long read hybrid |