Crazy high file size for human genome from Ensembl

Question

[Adrian Pelin]

Hello,

When I download release 95 repeats soft masked file "ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz" it is ~1 Gb, however if I decompress it, it becomes 54 Gb.

This is curious as the same soft repeat masked mouse genome decompressed is 2.7 Gb. Any idea why the human genome is so large and if there is any tool to reformat the fasta file into a smaller one?

Thanks, A

Answer 1

[Emily]

There are huge numbers of haplotypes in the human GRCh38. In the toplevel DNA sequence files these are represented as the whole chromosome, where most of it is Ns and only the haplotype sequence is actual sequence. This means that the compressed files aren't huge, as they just need to encode how many Ns there are, but decompressed are massive with all the Ns represented.

[Adrian Pelin]

That makes a lot of sense! So if I just download the "primary_assembly" I would have a smaller decompressed file size only at the expense of haplotypes, is that a fair prediction? Thanks

[Emily]

Yes, that is absolutely right.