GRCh37.p13 download at NCBI FTP?

Question

[Marvin]

I'm lost at the NCBI FTP server. Which file contains all chromosomes of GRCh37.p13 in one fasta? The program that I want to use takes one fasta file as the reference sequence. At ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ARCHIVE/ I don't see GRCh37.p13 and I don't see a README file .. I'm a little bit stuck here.

[ATpoint]

You can get it from Ensembl ensemble =), downloading Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz. Still GRCh19 is old. Any reason you do not go with GRCh38?

[Emily]

No, you can't get it from ensemble, but you can get it from Ensembl.

[ATpoint]

Yes Ma'am. Apologies for my carelessness ;-)

[Marvin]

I know how to get it from ensembl, I was curious where NCBI hides the equivalent :-)

[cpad0112]

Download GRCh37.p13 single fasta file from Gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz

or from here with index as well: http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch37/

Answer 1

[Kevin Blighe]

The NCBI record for GRCh37.p13 (GCF_000001405.25) can be found here: https://www.ncbi.nlm.nih.gov/search/?expt_dict=b&term=grch37.p13.

Click on Download and then select Genomic FASTA and RefSeq:

The tar file contains the complete NCBI version of the genome release in FASTA format.

Kevin

NB - FTP site is here: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/

[Dan]

When I try this method I get 'Estimated size is 0', and the resulting file has no data. This may be a temporary glitch I guess?

[Dan]

Ahh... Google search for download grch37 leads me to this URL: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ where the download is broken, but using your URL I get to: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/ the download works... I guess it's an issue of NCBI messing up their sitemap. ... Not sure why everything is broken today.

[GenoMax]

Unless you needed NCBI's version specifically, place to get original genome builds is GENCODE. They release official human genome builds.

[Sruthi]

Yes, thank for the link (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/). It works as of March 2024.