Question: retrieve the properties of the reads on NCBI on the command line
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gravatar for Chvatil
3 days ago by
Chvatil50
Chvatil50 wrote:

Hi everyone, I was wondering if anyone knows a quick way by command line to find information on the reads used for an assembly, by information I mean especially if it was paired end or mate end since if it is only an assembly made by pairend I will use Reapr in order to break missasemblies scaffols.

I need this information for several hundred assemblies, here is an example:

GCF_000002325.3

I guess fetch would be fine but does someone know how to use it in order to get this information?

Thanks for your help and see you soon

ncbi assembly reads • 54 views
ADD COMMENTlink modified 3 days ago • written 3 days ago by Chvatil50
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