Get sequencing informations from NCBI with acc number
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13 months ago
Chvatil ▴ 60

Hello everyone, I would need help using esearch.

I have a list of genomic accession number such as :

GCA_001442555.1 Apis_cerana
GCA_000469605.1 Apis_dorsata
GCA_000184785.2 Apis_florea
GCA_003254395.2 Apis_mellifera

and I would like to get informations about the sequencing and get for exemple :

Submitter,Date,Assembly method, Genome coverage et Sequencing technology.

Acc_nb            Sp_name Submitter Date Assembly_method Genome_coverage Sequencing_technology 
GCA_001442555.1   Apis_cerana
GCA_000469605.1   Apis_dorsata
GCA_000184785.2   Apis_florea
GCA_003254395.2   Apis_mellifera

Does anyone have a code for that ?

esearch -db assembly -query GCA_000612105.2

ncbi Assembly efetch • 307 views
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You are on right track. Try esearch -db assembly -query GCA_000612105.2 | esummary and then parse information you need using xtract.

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@genomax thank you I can get element such a Coverage or date by using esearch -db assembly -query GCA_003254395.2 | esummary | xtract -pattern DocumentSummary -element Coverage LastUpdateDate but I cannot get informations avoir the Sequencing technology for instance do you know why?

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That is not present in summary.

$ esearch -db assembly -query GCA_000612105.2 | elink -target biosample | elink -target sra | esummary | xtract -pattern ExpXml -element Platform instrument_model
ILLUMINA
ILLUMINA
ILLUMINA
ILLUMINA
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ok thank you very much it helped a lot !

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