The assembly language source code (with comprehensive comments) for a reader using a PIC microcontroller is available from 'Microchip' in their "13.56 MHz RFID System Design Guide". The Microchip system uses Manchester encoding. The guide can be downloaded using the following link: RFID System Design Guide.
If you have access to it, The American National Standard for Information Technology - Radio Frequency Identification ANSI NCITS 256: 2001 has a great deal of information including examples of communications sequences at the packet level, a diagram of data communication timing, API code examples and much, much more!
I hope that the above-mentioned material is of use and best wishes for your project.
