genome assembly records not present in assembly_summary.txt
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12 weeks ago
sapuizait ▴ 10

Hi all

Gathered from various sources my lab has downloaded several E.coli assemblies from NCBI. Now, that I am looking to the data, I am trying to retrieve the metainfo. Even though for most of them I can get that from the assembly_summary file that can be downloaded from the NCBI FTP, there are some that do not exist even in the latest version of the file. Example: GCA_018564605.1 does not exist in the assembly_summary file but if I look for it in the NCBI portal, it is there! https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_018564605.1/ Is it because the record is not curated? How can I retrieve these?

Thanks

ncbi bacteria assembly • 441 views
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If you have the accession numbers can you not use something like eutils?

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12 weeks ago
GenoMax 144k

Can you clarify what metainfo you are referring to?

The accession that you refer to does exist in GenBank assembly_summary file.

$ grep GCA_018564605 assembly_summary_genbank.txt
GCA_018564605.1 PRJNA514245     SAMEA7577678    DAEFSU000000000.1       na      562     562     Escherichia coli        strain=110504014        110504014       latest  Contig   Major   Full    2021/05/27      PDT001039592.1  National Center for Biotechnology Information   na      na      https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/564/605/GCA_018564605.1_PDT001039592.1  from large multi-isolate project        na      na      haploid bacteria        5111194 5111194 50.500000       0       66      66       NCBI    NCBI Prokaryotic Genome Annotation Pipeline (PGAP)      2021/05/17      4979    4757    93      30286803
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(

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