Questions tagged [de-bruijn-graphs]

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Where does the choice of k = 51 for de Bruijn graphs of large genomes come from?

This question has also been asked on Biostars 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 ...
Sebastian Schmidt's user avatar
10 votes
2 answers

Extract sequence context of high-degree nodes in assembly graphs

I often use metaSPAdes to assemble short reads from human microbiomes. My simplified understanding of short-read de Bruijn graph assemblers is that they fail where ambiguous paths cannot be resolved. ...
acvill's user avatar
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35 votes
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Why do some assemblers require an odd-length kmer for the construction of de Bruijn graphs?

Why do some assemblers like SOAPdenovo2 or Velvet require an odd-length k-mer size for the construction of de Bruijn graph, while some other assemblers like ABySS are fine with even-length k-mers?
Kamil S Jaron's user avatar
14 votes
3 answers

How to make a distinction between the "classical" de Bruijn graph and the one described in NGS papers?

In Computer Science a De Bruijn graph has (1) m^n vertices representing all possible sequences of length n over ...
Leo Martins's user avatar