Taxonomic NCBI is designed to annotate a Blast hit results file with each query sequence's description used to search a local copy of the NCBI taxonomy data. Once annotated the blast hit file can then be combined to a read count matrix file such that the resultant file contains both the sequences read counts in an array of samples and the likely taxonomic origin of the sequence.
Taxonomic NCBI is written to be flexible and so can process sequence descriptors from a range of sources such as the SILVA data set or standard GenBank sequence description. The only requirement for automated analysis is that the the descriptions have a roughly consist format.
As well as allowing the automated annotation of a file, Taxonomic NCBI will also allow you to perform manual searchers using either names (common English or Latin) or the species' NCBI taxonomy ID number.
The Taxonomic NCBI guide is here.
The compiled program can be downloaded from here.
Taxonomic NCBI can run on arrange of non-Windows PCs as described here.