I am comparing variants (mainly SNPs) identified in different S. cerevisiae strains and obtained using different sequencing technologies (i.e. Illumina NextSeq 500 and Proton). I found many discrepancies in variants identification on the same strain and I would like to know if this is due to the sequencing technologies or if this is determined by a poor filtering strategy in variants identification. Could you suggest studies performed on this topic? Alternatively, is there anybody having direct experience in this topic?
Thanks in advance.
Sincerely
--
Stefano Campanaro
PhD
University of Padova
Italy
Hi Stefano
You might find this paper useful. They used the Influenza Virus as a model system and highlighted the challenges that accompany NGS-based studies of viral diversity, especially in determining the minor variants. The validation methods and quality controls presented in the paper should be adaptable in any other model system.
https://jvi.asm.org/content/90/15/6884
Good luck
Dear Pritam Kumar Panda,
Thanks a lot for your answer, we will check this Vardict software and also other that you suggested.
We are also planning to try this new tool named "ForestQC", did you check it?
https://github.com/avallonking/ForestQC
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