Table 1.

List of tools specific to RNA-derived small RNA (tDR) identification.

Name	Mapping to	Potential Effects	Mapping Tools	Mismatches, Indels, and Chemical Modification	tDR Types Detectable	User Interface
Telonis et al., [32,50]	Genome to exclude reads mappable outside tRNAs	Potential false negative	–	Mismatches/indels not allowed	All four tRF types	No packaged pipelines provided
tDRmapper	tRNAs alone	Potential false positive	Built-in algorithms	Error type hierarchy	Multiple tRFs and tRNA halves	Command line
tRFfinder	First to genome and known transcripts, then to tRNAs	Moderate false positive & negative	bowtie/bowtie2	Allowed (with options), but given different weights (scores) in result page	Multiple tDR including all tRF types	Website interface