In our institute, we are going to establish a Genomic platform (Illumina). For data analysis and storage, what are the minimum requirements in terms of "computer setting (HPC)" using sequencing equipments such NextSeq and NovaSeq (I am biologist) ?
Thank you
It depends on what you are going to do.
1) Sequence some parts of genomes and then only map reads on the reference, several Tb of storage and 16-32 Gb of RAMs will be enough;
2) Sequence and assemble new small genomes (e.g. bacterial), then several Tb of storage and more than 32-64 Gb of RAM;
3) Sequence human genomes or exomes, then tens of Tb for storage, and 16-32 (for minimal work) or more (for comfortable work) of RAMs
Thank you Andrey,
You mean at least 64Gb RAM if dealing with human genomes or exomes.
Sequencing human genomes or exomes is probably our future applications.
the first and most important thing is:
to teach everybody to use loss free compression of the data e.g. using gzip !!!
most people underestimate how much cost that is saving: e.g. the raw data goes down by ~80% without loss. a typical DNA-only-sequence gets down by about 70-75%.
also consider what and when to throw raw data away and consider a strategy for when it is cheaper to create data again (e.g. making an experiment again) in respect to storage costs...
==> setup a clear strategy from the sequencing service, create a clear strategy for what users must do to help you keeping storage costs down AND educate the users to keep their local/private systems in order too (teach them how to compress their data on their local desctop...)...
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