I have a human fastq file from illumina Hi 2000. I want to assemble it on a reference genome, but i am confused what version of reference genome should i use hg19 or hg38. What is the criteria of choosing a reference genome version?
hg38 is currently the most used version. As mentioned before this has been present for quite some time now is stable. Finally it all depends on your goals. Your resources will also help decide which patch to use. I say this because, I intended to use the latest GRCh38p10 but I did not have the necessary computation power to index the whole genome; so I had to scale down to GRCh38p5 for which index was already available.
For details do refer: https://cofactorgenomics.com/choosing-a-reference-for-your-rna-seq-experiment/
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version 2.3.6
If you are actually going to do reference guided assembly then you should use hg38. That assembly has been available for a number of years at this time.
I think you mean alignment, not assembly, is that right? Hg38 is more complete, but not all annotation and variant databases are available.