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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