Cooja is the default simulator of the well known Contiki Operating system. Contiki implements IP for constrained nodes. If you are willing to test new protocols for IP_enabled nodes, Cooja is a better choice than NS2 or OMNET. Several research results have been published based on Cooja and Contiki.

Yes you can use it. However, I would recommend you to use any of the following well known simulators so that your simulation results are more reliable. Moreover, you would be able to get external help in case you require it.

A few well known simulators are:

1. OMNET++ with INET framework

2. NS-2, NS-3

3. OPNET (license required)

The following paper provides an overview and comparison of the well known simulators.

https://www.researchgate.net/publication/234018317_A_Performance_Comparison_of_Open_Source_Network_Simulators_for_Wireless_Networks?ev=prf_pub

Conference Paper A Performance Comparison of Open Source Network Simulators f...

Cooja is the default simulator of the well known Contiki Operating system. Contiki implements IP for constrained nodes. If you are willing to test new protocols for IP_enabled nodes, Cooja is a better choice than NS2 or OMNET. Several research results have been published based on Cooja and Contiki.

Hello, Can we use Cooja and Omnet together? somehow mix them together??

For wireless sensor networks, I prefer you to use NS2 or NS3 but if you are not satisfied with NS2 then you can try OMNET or opnet if you can afford the cost of opnet

@shirin, I think for that you have to write a code so that they can be interfaced between each other, I am not sure but may be it works

@Atta, can i use OMNET++ to simulate wireless sensor network which nodes are based on Contiki operating system?

I think NS-2 is one of the best simulator to simulate new or existing protocols in MANETs and WSN.

YES, you can use COOJA simulator to implement and simulate WSN Algorithms, COOJA provides real environment  to build your WSNs with different type of Motes, and you can test your work with different motes such as Tmote Sky, MicaZ and others. just by upload your same code to the mote, with no any modifications  between one mote to others. also COOJA has a different plug-ins that will help you to get  relevant results.   

Hello, please help! How can simulated Cooja moted with Java be added to Cooja simulation

Cooja  simulator  helps to understand  the protocol implementation in iot

castalia is also a good option

Cooja is the default simulator for WSN for Contiki OS. If you are willing to test new protocols for IP_enabled nodes, Cooja is a better choice than NS2, QUALNET or OMNET. Several research results have been published based on Cooja and Contiki.