At the least, you can use NR to prototype the processing you need to do. As you are restricted by the source device to only ever getting the whole file, this seriously limits what you can do. Normally, the way to get round this is to process the file as a stream - I think there may be some nodes to work with big files though I'm not sure how maintained they are.
Alternatively, something like the AlaSQL nodes may help as you can leverage AlaSQL itself to treat the file as a database.
And, as a final resort, write a small utility in Node.JS that grabs the file to disk and then trims it. You can call that from Node-RED passing in a timestamp perhaps to aid in the trimming. You could even extend that to write to a DB. Again, AlaSQL might help you there, it is a Node.JS module.
If you want to do that using shell commands, you can drive all of it from NR in the way that Dave has suggested.
So lots of options, it is a case of using the right tools for the job. If nothing else, NR is great at coordinating those activities in a more visual way.