How to get the DNA type information of bacterial genomes in batch?

[nkuyfq]

I am trying to generate metagenomic reads from some bacterial genomes randomly select from a list of NCBI RefSeq Bacteria. As the reference genomes are randomly selected, it's unlikely for me to manually search the DNA type one by one. How could I obtain the information about circular OR linear chromosome required by the option '-dl DNA_TYPE_LIST' in batch?

Many thanks!

[lcoombe]

Hi @nkuyfq,

To automate the process of getting the topology information from the NCBI RefSeq accessions, you could try using Entrez esearch - for example:

[lcoombe@hpce704 family]$ esearch -db nuccore -query "NC_003197.2" | esummary | xtract -pattern DocumentSummary -element AccessionVersion,Topology
NC_003197.2	circular