Reference selection
===================



Genotype detection
##################

Genotyping is important at different stages of sequence analyses. It can be used for determining 
the best reference to use for a reference assembly or to determine whether the sample has a 
mixture of different genetypes. 

MIRNA_SEARCH
************

`MIRNA\_SEARCH https://github.com/centre-for-virus-research/VATK/tree/master/GenotypingTools`_ is 
used in the HCMV pipeline to determine whether a particular sample has a mix of different 
genotypes.


Reference selection
###################


De-novo assembly
################