Retrieving organism name
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2.4 years ago

Hi,

I usually use the following command to get GCF_id (Accession) from the NCBI. How Can I retrieve the "organism name/source" from NCBI?

cat NZ_id.txt | while read i; do elink -db nuccore -id $i -target assembly|esummary|    xtract -pattern DocumentSummary -element AssemblyAccession ; done

Cheers

Assembly NCBI e-utlilities • 494 views
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1
Entering edit mode
2.4 years ago
AK ★ 2.0k

Changing from -element AssemblyAccession to -element Organism or -element SpeciesName will do.

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