I am trying to do taxonomy classification for my unmapped (to reference genome) reads. I tried both Megan (http://ab.inf.uni-tuebingen.de/software/megan5/ ) and kraken(http://ccb.jhu.edu/software/kraken/ ).
In kraken I can use read files directly as the input, whereas in Megan I have to make the blastN file first from the read files to give it as the input.
No plotting tool is readily available for kraken, while Megan already has a plotting tool.
I used bacteria,virus and fungi genomes as reference database. I am trying to figure out if I can use read files directly as an input to MEGAN so that I can skip the BLASTN step.
I also want to compare the Megan and kraken output.