will different pair-end reads length affect assembly?

[sequensized_simo]

Hi, I am a newbie in assembly, and currently get a set of pair-end reads to do some de novo assembly. The problem is I get one end of my reads having 44bp, and the other end has 46 bps. Do both ends have to have the same length to not affect the assembler's work? I assume it's not gonna to hurt the kmer hashing part, but not sure if it's gonna to hurt other steps built in any assemblers.

Appreciate for any helps and comments! Thanks!

Simo

[gaffa]

What you could do is just to run once with these lengths, and then once with the second pair trimmed down to a length of 44 bp as well, and see how it affects the results.