Table 1.

Features of different resistome analysis pipelines, in comparison to sraX.

Bioinformatic	Standalone	SNP	Gene context	Batch	Single-step	Output	References
tool	mode	analysis	analysis	mode	command	results
CONTIG-ASSEMBLED SEQUENCE DATA
ResFinder	Yes	Yes	No	Yes	Yes	Tables	Zankari et al., 2012
ARG-ANNOT	No	Yes	No	No	No	Tables	Gupta et al., 2014
RAST	Yes	No	No	No	Yes	Tables	Davis et al., 2016
RGI	Yes	Yes	No	No	No	Tables/Plots	Jia et al., 2016
PointFinder	No	Yes	No	Yes	Yes	Tables	Zankari et al., 2017
ARGs-OAP	Yes	No	No	Yes	No	Tables/Plots	Yin et al., 2018
NCBI-AMRFinder	Yes	Yes	No	Yes	Yes	Tables	Feldgarden et al., 2019
sraX	Yes	Yes	Yes	Yes	Yes	Tables/Plots	Present study
RAW-READS SEQUENCE DATA
SRST2	Yes	Yes	No	No	Yes	Tables	Inouye et al., 2014
Mykrobe predictor	Yes	Yes	No	No	Yes	Tables	Bradley et al., 2015
SSTAR	Yes	No	No	No	No	Tables	de Man and Limbago, 2016
SEAR	Yes	No	No	No	Yes	Tables/Plots	Rowe et al., 2015
KmerResistance	No	No	No	No	Yes	Tables	Clausen et al., 2016
PATRIC	No	No	Yes	Yes	No	Tables/Plots	Antonopoulos et al., 2017
ARIBA	Yes	Yes	No	No	No	Tables/Plots	Hunt et al., 2017
GROOT	Yes	No	No	No	No	Tables	Rowe and Winn, 2018
DeepARG	Yes	No	No	No	No	Tables/Plots	Arango-Argoty et al., 2018

Bold characters emphasize the functional features of the proposed tool.