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.
1 answer
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/
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.
Yes, thank for the link (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/). It works as of March 2024.
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You can get it from Ensembl
ensemble=), downloadingHomo_sapiens.GRCh37.dna.primary_assembly.fa.gz. Still GRCh19 is old. Any reason you do not go with GRCh38?I know how to get it from ensembl, I was curious where NCBI hides the equivalent :-)
No, you can't get it from ensemble, but you can get it from Ensembl.
Yes Ma'am. Apologies for my carelessness ;-)
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/