switching from illumination to NEB prep kits
Hi all, we already have built some pipelines for germline / somatic calling on WES data ( the library prep kits used were from Illumina).
now we want to switch to using NEB library kits, and I would like to know (rom a bioinformatics point of view) if there anything I should know before moving to this step f ?
I guess the same pipelines can be stilll used, only the adapter trimming step might change, but other than that, using a different library prep kits should not have any extra impact on the processing steps right ?
Many thanks for your help.
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If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter then you will use that in processing.
If you are using a different exome capture kit then the areas of the genome covered may be different and the results may be slightly different as well. You will want to run a few samples that were done with the old kit through the new one to test concordance.