04/07/2018: version 1.3.1 (7/18): current sRNAde.jar

Bugfix: Fixed an error when calculating differential expression using an expression matrix as input. The program died prior to the analysis when the grpString parameter was not specified (which is only needed if the input consists of sRNAbench output folders)

12/06/2018: version 6/18 (version 1.5): current sRNAbench.jar


  • adapter trimming: random adapters can now be specified and eliminated
  • improved assignment of family names of novel microRNAs
  • improved error handling
  • tRNA fragment detection with ‘tRNA=’ tag


reads.annotation: the all reads mapped to a certain microRNA had the cooridnates of the canonical sequence (miRBase or miRGeneDB entry). Now the coordinate of the read relative to the precursor start position is given

12/06/2018: version 6/18 (version 1.3):

Novelties: Several new isomiR reletated analysis

12/06/2018: New Virtual Machine version: current VM


Populate tool: this tool does now reconnect automatically resuming interrupted downloads. Before, after interruption, the interrupted files needed to be removed restarting the download manually.


The update tool (to obtain the newest version of the tools) was broken but works now again

30/5/2017: Version 6/17 released:

Novelties: prediction of novel microRNAs was improved, command line help was added, statistics of genome mapping (if more than one species was used)

30/5/2017: Version 6/17 released:

Novelties: command line help was added, new features as expression matrix from fasta files, isomiR analysis at a read level

15/8/2016: Version 08/16 released: sRNAbench.jar

15/8/2016: Version 08/16 released: sRNAde.jar


SRNAbench: 30/05/2017

For microRNAs that map both, to the forward and negative strand (like hsa-miR-486-3p) the adjusted read count was calculated incorrectly (taking into account the mappings to the negative strand). This bug was fixed now.


Virtual machine

22/03/2018: new virtual machine released (problems with bowtie that affected sRNAbench were fixed)

21/11/2017: new virtual machine released (problems with R modules that affected sRNAde were fixed)

31/05/2017: new virtual machine released (big-indexes are now recognized automatically, new versions of sRNAbench and sRNAde included)