Illumina would be a best and cost effective solution. But you must look into the size of your amplicon since it is limited to the max 300 bp size. With the choice of right strategy, you can multiplex upto several hundred samples.

Dear Arun

I agree with the previous answer that Illumina platform might be the best solution given the accuracy of the sequencing and the number of sequences you can produce in one run. The kind of approach and cost depends on your specific goals.

For instance if you are using DNA barcoding for species identification you could try to perform 18S sequencing with Illumina and then classify your samples (as it is done in metagenomics studies). Developing probes for few genes might be expensive so if you don't think that 18S might be useful, then you could try with a "shallow" whole genome sequencing to perform a raw de novo assembly that might be enough for species identification. Depending on the approach the cost could be around 100-200 euros per sample (or more for more advanced approaches).

If you would like more information, please send me a private message since where I work we offer sequencing and bioinformatics data analysis and we might help you with your project.

Have a nice day

Riccardo

Bioinformatics data analyst at www.sequentiabiotech.com

Tanks Dr. Abhijeet Singh and Dr.Riccardo Aiese Cigliano for your valuable response. Still waiting for more information from different experts so that I could reach at any conclusion and proceed further.

Regards

Arun