How to download a genome assembly from the NCBI website?

Question

[biomagician]

I would like to download the genome assembly described in

https://www.ncbi.nlm.nih.gov/assembly/GCA_016989235.1

but when I click on "Download Assembly", I get a directory without the genome assembly. The README present in it did not help me.

What puzzles me is that when I use the link from another Biostars question

https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2

and download the assembly, the FASTA file is there. This makes me believe that there is something wrong with the link to the Caenorhabditis elegans assembly:

https://www.ncbi.nlm.nih.gov/assembly/GCA_016989235.1

How can I get the C. elegans assembly?

Answer 1

[patrickdm]

Hello, you can get it from the Download tab in

https://www.ncbi.nlm.nih.gov/Traces/wgs/JAFETV01?display=contigs

(following the WGS projects link in https://www.ncbi.nlm.nih.gov/assembly/GCA_016989235.1 and then the last WGS JAFETV010000001-JAFETV010000073 link in the new page loaded)

Answer 2

[SushiRoll]

Hey biomagician!

I have tried the first link and after doing "Download assembly", I selected Genbank as the source. The downloaded file is a .gz, you'll need to decompress it. There is an additional directory with another gz compressed file called GCA_ ...... after decompressing it, you should get your fasta file.

Hope it works!

Answer 3

[GenoMax]

As you discovered the "RefSeq" version for this assembly does not seem to work (GenBank one does) when using Download Assembly button (could email NCBI help desk and let them know).

You can get the GenBank version here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/989/235/GCA_016989235.1_MY2147_Canu/GCA_016989235.1_MY2147_Canu_genomic.fna.gz

RefSeq version can be accessed directly: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/Caenorhabditis_elegans/latest_assembly_versions/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.fna.gz