DECONTAMINER HTML REPORT EXAMPLE

Here you can access the html reports that decontaMiner automatically generates at the end of the pipeline. The results are obtained running the whole pipeline on the three test bam files (available in the download area of the main page).

Pipeline details and settings. The bam files contain single end data, hence the pipeline has been run with the -s parameter set to S . The last step of the pipeline (i.e. the results filtering) was performed with a match count (MC) threshold of one hundred, i.e. -t 100. All the other parameters were left unchanged (see default values in the user guide). The input was processed to detect contamination coming from bacteria, fungi and viruses.

Results details. The html reports generated by decontaMiner are available for each database of contaminating sequences. For fungi and bacteria the report is generated grouping the resulting organisms both for genus ( ge ) and for species ( sp ). The main page contains information on the whole dataset. By clicking on the sample name in the overview graph it is possible to access the detail page for each of the sample.

 

Please use the following links to access the html result pages: