Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum

Table 1 List of non-proprietary isomiR alignment programs

Program	Usage	Alignment method	Publisher
isomiR-SEA 1.60	Command line isomiR-SEA_1_6 -s tca -l 10 -b 4 -i < in_path > −p < out_path > −ss 6 -h 11 -m < mature_mir_file > −t < countfile>	User-defined seed size (default 6)	Urgese et al. [21]
isomiRID 0.53	Command line standard config file	bowtie1	de Oliveira et al. [22]
miraligner 3. Feb 2016	Command line java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s tca -freq	8 nt seed	Pantano et al. [23]
IsomiRage	Desktop GUI	bowtie1	Muller et al. [24]
DeAnnIso	Webapp	bowtie1 and BLAST	Zhang et al. [25]
isomiRex	Webapp	bowtie1	Sablok et al. [26]
miR-isomiRExp	Webapp – offline	bowtie1	Guo et al. [27]

The three command line tools were used for our comparative evaluation. The others were discarded because they were incompatible with local high-throughput pipelines

ISSN: 1471-2105