What is the best tool to classify my contigs. I have at least two species not represented in the databases for which I have the reference sequences, I would like to use the reference sequences to classify the contigs, ideally showing the % match to the reference.
Then after I have the contigs that matched the reference, what is the best tool to map the reads to the contigs to get a good estimate of how many reads align to the contigs, ideally getting a Reads Per Million count.