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From hearsay I know that de Bruijn graphs of large genomes (e.g. human) are usually constructed with k = 51, or that k = 51 is at least a good initial choice.

I however am unable to find any source for this, does anyone know where it is coming from?

  • 2
    $\begingroup$ Not an answer. SGA is the first assembler I know that has a 51-mer default (more exactly ≥51bp overlap) but I am not sure if k=51 comes from SGA. Note that ALLPATHS-LG/DISCOVAR, arguably the best short-read dBG assembler for large genomes, uses k>100 for end-merged reads, so I don't think k=51 is necessarily an optimal choice. $\endgroup$
    – user172818
    Aug 3, 2022 at 13:26
  • $\begingroup$ Note that k should (must?) be odd to avoid kmers that are reverse-complement palindromes. $\endgroup$ Aug 4, 2022 at 19:07


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