retrieve the properties of the reads on NCBI on the command line
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12 months ago
Chvatil ▴ 60

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:


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

Assembly reads ncbi • 224 views

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