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Unable to retrieve the "Assembly method" of an assembly using Edirect in the terminal

Dear all , I am having a list of assembly ID and would like to retrieve specific info on the assembly method (eg. SPADes) from the docsum of that assembly. I have been trying these codes that worked for some other retrievable info, but I could not find the Assembly method although it is shown on the ncbi website. I also inspected the docsum itself where I can not find assembly method. I still see some tutorial using some commands as shown below but it did not work. Here is my code:

printing the docsum

esearch -db assembly -query "GCF_037000505.1" | efetch -format docsum

I looked into this, there is no assembly method

Some tutorials suggested

efetch -db assembly -id GCF_037000505.1 -format docsum | xtract -pattern DocumentSummary -element AssemblyMethod

This did not produce any output.

Can you advise on a way in linux using esearch to retrieve the assembly method ? Why it is not retrieved via docsum although present on ncbi ?

Thanks

assembly sequencing genomics
• 1,383 views • link
written by Mohamed Samir • Mohamed Samir

I not sure, but when I used the same code to retrieve other info (e.g. AssemblyStatus), it came out correctly as shown in the docsum !

• 0 views • link
written by Mohamed Samir • Mohamed Samir

You can only extract things shown in docsum output which does not contain this info.

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written by GenoMax GenoMax

1 answer

Using datasets and dataformat tools from NCBI:

$ datasets summary genome accession GCF_037000505 --as-json-lines | dataformat tsv genome --fields organism-name,assminfo-assembly-method
Organism Name   Assembly Assembly Method
Klebsiella pneumoniae   SPAdes v. 3.7
• 0 views • link
written by GenoMax GenoMax

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