Table 2 Recommended strategies for generating high-quality haploid assemblies
From: Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
Assemblers | Recommended strategies | Advantages |
|---|---|---|
Canu | purge_dups and/or purge_haplotigs | Highest N50 (Nanopore) |
Flye | purge_dups | |
NextDenovo | read filtering, purge_dups and/or purge_haplotigs | High continuity |
Ra | read filtering | Low RAM usage and CPU time |
Raven | read filtering + purge_dups or purge_dups + purge_haplotigs | Low RAM usage and CPU time |
Shasta | purge_dups | Low CPU time |
wtdbg2 | purge_haplotigs | Lowest RAM usage and CPU time |