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Lz4

LZ4 is a lossless data compression algorithm that is focused on compression and decompression speed

Snappy

Snappy is a compression algorithm for byte streams and a library implementing this algorithm



Others

Example

Lz4 is probably better though snappy was developed by google with protobufs in mind so you might want to test both on your data set.

from question  

Improving performance of protocol buffers

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