Find Best References using Read Mapping

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)

The Find Best References using Read Mapping tool takes one or several single or paired-end read sequence lists as input. It then maps simultaneously against a set of references, and optionally a set of host references. The tool will output a list of the references identified. The host references can be used to filter away contaminated reads (e.g. a human reference). The tool can also output the read mappings for both the references and the host.

After specifying the input reads, it is possible to specify the references and adjust the detection parameters, see (figure 10.6).

Image find_best_references_using_readmapping_step1
Figure 10.6: Select references and filtering options.

The following parameters are available:

The next step is to specify the read mapping options (figure 10.7). These options are identical to the ones used by the Map Reads to Reference tool.

Image find_best_references_using_readmapping_step2
Figure 10.7: Select read mapping options.

The final step is to select which output objects to produce.