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How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?

A few questions regarding the -g genome-size argument for Flye and MetaFlye:

  • How much does this value influence the performance and output of the assemblies?
  • How can I estimate the genome size for a metagenome or a genome whose size is unknown w/ no close representatives?
  • Is there a (third-party?) tool used by Flye or Metaflye that can estimate this value?
assembly fasta genomics nanopore pacbio
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updated by akshay • akshay • written by O.rka O.rka

1 answer

I dont think you need to provide genome size estimate for metaflye.

For Genome assemblies genome size is typically estimated from short reads or approximated based on available information regarding the genome size of the organism or its close relatives.

  • The assembly created from the run wont be exactly the genome size input. I think It is an initial guess for the algorithm.
  • Jellyfish+genomescope if you have short reads.
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written by akshay • akshay

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