Create Taxonomic Profiling Index

This tool will compute a a taxonomic profiling index from a reference database. Indexes are then used as input to the Taxonomic Profiling tool. The computation of index files for taxonomic profiling is memory and hard-disk intensive due to the large sizes of reference databases usually employed for this task. The algorithm requires roughly the number of bases in bytes of memory (as indicated by the Download Custom Microbial Reference Database tool), i.e., approximatively the size of the uncompressed reference database; and twice this amount in hard disk space.

Image taxproindex
Figure 15.1: Select sequence lists with the references of interest.

To run the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Databases (Image databases_folder_closed_16_n_p) | Taxonomic Analysis | Create Taxonomic Profiling Index (Image taxonomyindex_16_n_p)

As input, select one or more sequence lists containing the references of interest. These can be downloaded for example using Download Custom Microbial Reference Database (Download Custom Microbial Reference Database).

The tool makes use of Assembly IDs (see Using the Assembly ID annotation) in combination with either Latin name or, if Latin name is not present, Sequence name. The tool will treat sequences as one reference, if they have:

The output is an index file and a report as seen in figure 15.9. The report list the number of sequence and basepairs that were indexed.

Image taxproindex1
Figure 15.2: The reference sequences,index and report as seen in the Navigation Area.