Find Best References using Read Mapping

The Find Best References using Read Mapping tool maps reads to a reference sequence list to identify the best matching reference i.e., the references for which the input reads hold more evidence.

If a host genome is provided, reads that map better to the host are filtered to not have them count toward results.

To start the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | Find Best References using Read Mapping (Image find_best_reference_w_mapped_16_n_p)

In the first dialog, select the sequences or sequence lists containing the sequencing reads, and click on Next.

In the References dialog, specify the following (figure 7.6):

Image find_best_references_using_readmapping_step1
Figure 7.6: Select references.

In the Mapping options dialog, specify settings for the read mapping (figure 7.7). The options are identical to those of the Map Reads to Reference tool and are described here:

Image find_best_references_using_readmapping_step2
Figure 7.7: Select mapping options.

The Filters dialog holds the following options (figure 7.8):

Image find_best_references_using_readmapping_step3
Figure 7.8: Select filtering options.

In the final step, specify the output: