PRAP: Pan Resistome analysis pipeline

BMC Bioinformatics

Table 1 Performance of different methods for ARGs identification

Input Format	Database	SMC	MCC	Runtime (min)
Raw Reads	CARD	0.9638	0.9809	25
Scaffolds	CARD	0.8954	0.9440	< 1
CDSs	CARD	0.9600	0.9789	< 1
Proteins	CARD	0.9532	0.9347	30
Raw Reads	ResFinder	0.9345	0.9649	25
Scaffolds	ResFinder	0.9924	0.9960	< 1
CDSs	ResFinder	0.9899	0.9946	< 1
Proteins	ResFinder	0.9647	0.9812	30

Parameters for the k-mer method included a k value of 25, two searching kernels, a depth of 20 and at least 100 area score and 90% coverage by length. Parameters for BLASTn and BLASTp included 95% identity for BLASTn and 98% identity for BLASTp and at least 90% coverage by length for both. Runtime is the time consumed for analyzing 26 genomes

ISSN: 1471-2105