Integrate Kraken into Proksee

[emarinier]

As it seems Mash does not easily provide per-read or per-contig classification, it will be difficult to perform contamination filtering using only Mash. In order to perform read-based and/or contig-based contamination filtering, we should implement Kraken into Proksee.

We should still leverage Mash in the early stages for species selection, and for recognizing from a very high-level the possibility of contamination.

[emarinier]

Integration of Kraken into Proksee will require more consideration, as Kraken may have memory requirements that make running Proksee increasingly difficult.