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I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
NC_030850.1
NC_030851.1
NC_030852.1
NC_030853.1
NC_030854.1
NC_030855.1
NC_030856.1
NC_030857.1
NC_030858.1
NC_030859.1
I need to download these FASTA files using the terminal because I'm working on a server. I'll be grateful if someone can help me. Thank you.
Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities
Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh
In the terminal, install it using: source ./install-edirect.sh
Then, you can download your sequence by doing:
esearch -db nucleotide -query "NC_030850.1" | efetch -format fasta > NC_030850.1.fasta
And you should find your fasta sequence downloaded.
As you have several sequences to download, I think it will be quite easy to add this command into a little bash script to process all of them.
More readings about that: http://bioinformatics.cvr.ac.uk/blog/ncbi-entrez-direct-unix-e-utilities/ and https://www.ncbi.nlm.nih.gov/books/NBK179288/
NCBI_API_KEY for batch downloading with GNU parallel at a max rate of 10 sequences/s. Then save accessions in one file and run parallel -a accession.txt -j8 'efetch -db nuccore -id {} -format fasta >{}.fa'. Adjust -j8 to -j3 if you do not have a key.
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Dec 6, 2022 at 7:57
Just wget or curl each as https://www.ncbi.nlm.nih.gov/nuccore/NC_030853.1?report=fasta&log$=seqview&format=text...
curl -L 'https://www.ncbi.nlm.nih.gov/nuccore/NC_030853.1?report=fasta&log$=seqview&format=text' downloads a HTML page with an (invisible) form on it, not a FASTA file.
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May 27, 2021 at 15:30
The best way to download FASTA sequences for an entire genome is to search for the genome, for example Theobroma cacao genome in the NCBI Assembly portal and use the big blue Download button.
For a given assembly, if you want to download the FASTA sequences for a bunch of chromosomes, you can do that by going to the Genomes FTP path highlighted in the screenshot:
Once you are in the Genomes FTP path, you can navigate to the FASTA folder as follows:
Theobroma FTP directory >> Assembly Structure >> Primary Assembly >> Assembled Chromosomes >> FASTA.
For this, you can use Entrez Direct as mentioned by @dc37. Why not always use Entrez Direct? While it is fine for a small number of sequences, it can be slow to download a large number of sequences. Entrez Direct by default will download uncompressed data so you will end up spending more time downloading a larger file instead of downloading a smaller, compressed file from FTP more quickly.
If you were to use Entrez Direct for this purpose, I'd not bother with a bash script and use epost to first post the entire list of accessions and then pipe it to efetch as shown below:
epost -db nuccore -input <file_with_accs> -format acc \
| efetch -format fasta > sequences.fasta
1061361601Use the ID in the query string to download directly:
https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=1061361601&db=nuccore&report=fasta&retmode=text&withmarkup=on&tool=portal&log$=seqview&maxdownloadsize=100000000
You can also get this link directly, by using Chrome's developer tools (F12), viewing the Network tab, then loading the page in (1).
(Sorry, I can't post a comment with my reputation score).
@vkkodali, interesting command I did not know about it ;). However, your command is downloading all sequences from the input file into a single fasta file. I believe that if you have a big bunch of sequences, it could be a little bit tricky after to manipulate that kind of file. Just by curiosity, do you have a trick to create one sequence per file using efetch ?
epost and efetch; you will have to either use a bash script or postprocess the efetch output using the unix tool split.
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