Body: <p><em>This question has also been asked on <a href="https://www.biostars.org/p/9533382/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>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.</p>
  <p>I however am unable to find any source for this, does anyone know where it is coming from?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-03T13:26:21.447Z
Comments.Text: 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.
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-04T19:07:45.117Z
Comments.Text: Note that `k` should (must?) be odd to avoid kmers that are reverse-complement palindromes.
Comments.UserDisplayName: Darlingtonia
Tags: <de-bruijn-graphs>
Title: Where does the choice of k = 51 for de Bruijn graphs of large genomes come from?
ThreadText: # Where does the choice of k = 51 for de Bruijn graphs of large genomes come from?
  
  (Asked by: username_0 on 2022-08-03)
  
  *This question has also been asked on [Biostars](https://www.biostars.org/p/9533382/)*
  
  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?
  
  **Tags:** de-bruijn-graphs
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: Note that `k` should (must?) be odd to avoid kmers that are reverse-complement palindromes.  
  
  ---
  
  ## 0 answers
  
  