is there any difference between size of RefGenome in UCSC and Ensembl?

Question

[star]

I have downloaded the Human Refrence Genome from Ensembl and UCSC like below:

UCSC: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

and when I make the uncompressed using gunzip, I get a different size like:

                      Zip       Unzip
 UCSC                938 M      3.1 GB
Ensembl             1.0 GB      62 GB

I would like to know is there anything wrong? Because I would like to make an index for aligning and if I use UCSC it takes ~ 1 hour while Ensembl takes 11 hours.

[Pierre Lindenbaum]

Difference between UCSC and Ensembl genomes

Difference between the Fasta files from UCSC and Gencode/Ensembl

Answer 1

[GenoMax]

toplevel assembly file you have above includes

all sequence regions flagged as toplevel in an Ensembl schema. This includes chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions.

This file is 60G. See this README file for more details.

Normally primary assembly is sufficient for most analyses. This is included in Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz. This should be more or less equivalent to UCSC download you have.