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Amazon Athena, is a distributed that will allow you to use SQL to query S3 data in place.
There are no pre-defined limit on size of data, yes it supports joins and you can find supported data format here.
To understand how to create tables for Athena (only metadata, data is not moved) please refer to this documentation page.
For additional information you can look at the FAQ.
If you are already using Amazon Redshift it also can access data in place from S3, using Amazon Redshift Spectrum.
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Thanks Fabrizio. Sorry, I should have mentioned that we are looking at tools other than Athena/Redshift to which S3 can connect using connectors. We are already using Athena/Redshift. Where can I get more information on S3 connectors? Please guide