How to get sample details from NCBI datasets

Question

[beginner123]

Hi, I have a list of assembly accession number like this GCF_000421605.1 GCF_001652585.1 GCF_012317585.1 GCF_011207455.1

How can I automatically get the sample details of these assemblies as a list?

[Pierre Lindenbaum]

use ncbi eutils: https://www.ncbi.nlm.nih.gov/books/NBK25500/

Answer 1

[vkkodali_ncbi]

You can do this using NCBI Datasets command-line tool. First, make a list of all the assembly accessions and use NCBI Datasets to download a package (we use --dehydrated flag to fetch only metadata and skip all sequence and annotation data). Then, use the dataformat tool to convert the assembly report from jsonl to a tabular format.

## input file
$ cat accs.txt 
GCF_000421605.1
GCF_001652585.1
GCF_012317585.1
GCF_011207455.1
## download using datasets 
$ datasets download genome accession --inputfile accs.txt --dehydrated
## contents of the datasets package 
$ unzip -v ncbi_dataset.zip 
Archive:  ncbi_dataset.zip
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
    1604  Defl:N      769  52% 2022-06-04 08:47 3de26d82  README.md
   12987  Defl:N     3514  73% 2022-06-04 08:47 53d1bc19  ncbi_dataset/data/assembly_data_report.jsonl
    4497  Defl:N      782  83% 2022-06-04 08:47 af0e24e7  ncbi_dataset/fetch.txt
    2522  Defl:N      385  85% 2022-06-04 08:47 38db1709  ncbi_dataset/data/dataset_catalog.json
--------          -------  ---                            -------
   21610             5450  75%                            4 files
## extract metadata into a table using dataformat 
$ dataformat tsv genome --package ncbi_dataset.zip > assm_tbl.txt

Note, the output table assm_tbl.txt is quite big with 95 fields. But it should be feasible to load the file into a spreadsheet app and filter data as needed. Alternately, if you are interested in only a specific set of biosample attributes you can use dataformat to extract only those. Finally, if you are conversant with JSON, you can use a tool like jq (https://stedolan.github.io/jq/) to conditionally extract only certain fields.