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.
Figure 15.1: Select sequence lists with the references of interest.
To run the tool, go to:
Toolbox | Microbial Genomics Module (
) | Databases (
) | Taxonomic Analysis | Create Taxonomic Profiling Index (
)
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:
- Identical Assembly ID and same Latin name, or
- Identical Assembly ID and same unique sequence name
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.
Figure 15.2: The reference sequences,index and report as seen in the Navigation Area.