Does 5' trimming of reads have an impact on the assembly?
Usually (with Illumina data) the quality drops at the end and that's where most of the trimming takes places, but we also regularly see quality turbulence in the first few bases.
I've been using Sickle for trimming and I'm very satisfied with the output. There is also an option for 5' trimming.
Would this 5' trimming cause problems with the insert size estimation, do assemblers assume an intact 5' end? Any experiences?
Usually (with Illumina data) the quality drops at the end and that's where most of the trimming takes places, but we also regularly see quality turbulence in the first few bases.
I've been using Sickle for trimming and I'm very satisfied with the output. There is also an option for 5' trimming.
Would this 5' trimming cause problems with the insert size estimation, do assemblers assume an intact 5' end? Any experiences?
