I would like to know pros and cons of different illumina assembly tools:
My first data set is 16S RNA illumina paired end bacterial sequences and second data set is metagenomic paired end illumina sequences. After some research I stuck with two tools.
2. CLC Genome workbench(commercial).
Is there any other tools which give us good results as illumina assembler?
I use velvet for de novo genome assembly but for metagenomc dataset meta-velvet would be a good option. There are lots of assembly tools out there to choose from but it's a good idea to use the most popular-ones beacause if you get stuck, you can get help from people who use these short-read assemblers regularly. Some people use SOAPdenovo, ABySS as well. Check out all the short-read assemblers available here in my website http://chandanpal.weebly.com/learning-resources.html.