Get reference full genome sequences for selected organisms

Question

[marongiu.luigi]

Hello,

I would like to download all the reference sequences, full length for a given organism. I am using esearch as reported on the NCBIwebsitee with the following command:

esearch -db "nucleotide" -query "txidX[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa

where X is the code for a given taxon. This works but I get both 'complete genome' and 'complete sequence' entries.

Is it possible to get only the 'complete genome' entries? Thank you

Answer 1

[Joseph Hughes]

This is most likely a result of your particular species having multiple segments or chromosomes. For example:

esearch -db "nucleotide" -query "txid40120[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa

would retrieve 32 complete genomes but

esearch -db "nucleotide" -query "txid4txid40051[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa

would retrieve 10 complete sequences, one for each of the 10 segments of the bluetongue virus.

So the approach to take depends on what you really want to retrieve.

[marongiu.luigi]

thank you, but the taxon I am looking for contains both complete genomes and sequences; still is there a way to separate them, either directly with an option of esearch or afterward with the manipulation of the resulting fasta file?