Hash Length, K-Mer Size, Word Size

Question

[maymay]

Hi, I am a novice in de novo assembly field. I keep coming across these different terms: hash length, k-mer size, word size when reading about different assemblers. I wonder if they are synonymous or if there are slightly different shades of meaning here...

[GAO Yang]

I think the k mer size is the same with the word size, although k mer is more popular~ Hash length is different meaning, it'll change according to the k-mer size and genome size.

[Leonor Palmeira]

For me, these three terms describe the same concept : a given length 'k' used to identify all observed successions of 'k' letters in reads. This is generally used for read indexing in assembly algorithms. Are you asking this in the context of a given assembly program, or in a general context?

[maymay]

I was asking this in general context - when reading literature I came across these terms used by different authors and wanted to confirm if they meant essentially the same thing.

[Leonor Palmeira]

If an author does not define clearly what is meant by one of these terms, then it is used in its generally accepted meaning, and these three terms are equivalent.

[maymay]

Thanks, Leonor! That is what I was hoping to hear...

Answer 1

[Tianyang Li]

Hopefully Velvet's author Zerbino's thesis can help.