I have assembled (using IDBA) illumina contigs for taxonomic classification. Is there any tool which can do the taxonomic classification of assembled illumina reads.
I used Megan in order to analyze data generated using blastn from both, contigs and reads that we were not able to ensemble. How can this be reflected in MEGAN or other tool? For example in the header id of contigs I know how many reads are used
and for the reads I have
I want to consider this information for example for compare samples and for rarefaction, shannon index, etc.
As I said, I tried MEGAN. But MEGAN is only considering the read counts.
Please give me some advise here.