Table 10.

Excerpt of the report table automatically generated by EAGER

Sample	# merged	% merged	# reads after C&M	# mapped reads	Duplicates
name	reads	reads	prior to mapping	prior to DeDup	removed with DeDup
3077	5,437,812	94.78 %	5,737,174	1,023,502	410,234
Jorgen625	12,956,100	80.5 %	16,093,580	2,659,178	94,005
Refshale16	32,041,091	73.61 %	43,528,407	12,782,665	3,872,555
SK2	51,364,343	99.27 %	51,741,310	48,211,553	47,353,377
SK8	7,683,942	72.5 %	10,597,941	1,227,067	185,913

The report shows results for five leprosy samples processed with EAGER. The number of merged reads, the percentage of merged reads as well as the number of duplicates removed can be seen for the respective samples. Note that this has been narrowed down to fit the page layout. A full report features more statistical values describing a sample, depending on which methods have been chosen to be executed in the pipeline (see Additional file 1)