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Mapping RefSeq accession to assembly ID

Hi,

Is there a way to map RefSeq accession to assembly ID (I need to do it for all the bacteria in RefSeq FTP site) ?

For example: NZ_KN150745.1 -> GCF_001640985.1

Thanks

refseq assembly
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updated by 5heikki 5heikki • written by lironyoffe • lironyoffe

2 answers

Unix eutils solution would be:

elink -db nuccore -id "NZ_KN150745.1" -target assembly|esummary|xtract -pattern DocumentSummary -element AssemblyAccession
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written by Sej Modha Sej Modha

The fastest solution besides parsing from the sequence files that you might have already downloaded would be to download the *assembly_report.txt files and parse from there,

e.g. 

awk 'BEGIN{FS="\t"}{if(!/^#/){print $7}}' GCF_000754995.1_PVA_assembly_report.txt
NZ_KN150745.1
NZ_KN150746.1
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written by 5heikki 5heikki

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