Download Assembled Genomes NOT in RefSeq
I have a list of NCBI accession numbers and I need to download the genome sequence (or assemblies) in FASTA format. I can accomplish this for genomes that are present in RefSeq using the following command:
esearch -db nuccore -query GCF_900343155.1 | efetch -format fasta > GCF_900343155.1.fasta
However, for some assemblies not in RefSeq and only in GenBank, the command returns an empty file:
esearch -db nucleotide -query GCA_012517935.1 | efetch -format fasta > GCA_012517935.1.fasta
I am able to download the GenBank assembly directly from the NCBI website, so I know it’s there.
Does anyone have a good idea of how to download specific genome assemblies that are in GenBank but not in RefSeq using these tools?
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