15/12/2021: New improvements to sRNAtoolbox website

  • New batch mode: The improved batch mode includes the option to import read files directly from the two major cloud services: Google Drive and Dropbox.
  • Reference annotations updated: 357 plant, animal or virus species from Ensembl annotations (166 supported in the previous version). PmiREN is also available now for more precise profiling of plant miRNAs.
  • sRNAcons new tool was included. Using a small RNA fasta file map them to the genomes in sRNAtoolboxDB and give back for each small RNA sequence its ‘conservation depth’.
  • sRNAde and sRNAblast were improved to make downloading relevant results easier. sRNAblast now includes a single assignment species detection graphic.

30/08/2021: sRNAtoolbox docker last version (0.0.4/latest)

New version of sRNAtoolbox docker release. Bugs of populate software have been fixed and the last version of sRNAbench.jar has been included.

15/07/2020: sRNAtoolbox docker release

sRNAtoolbox is available now as a docker image that can be download throught dockerhub ( This replaces the virtual machine, which from now on will not be updated.

02/07/2019: New sRNAbench publication

Several additions to our webserver included in our most recent publication: Aparicio-Puerta et al, sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression, Nucleic Acids Research,

  • A batch mode: unlimited number of input read files can be provided in different formats, as links or SRA run accession IDs.
  • New protocols supported: “NEBnext” from New Englands Biolabs, Nextflex from Bioo Scientific, SMARTer from Clonetech and sRNA-seq protocol with UMI (Unique Molecular Identifiers) from Qiagen.
  • Quality control of input fastq files
  • Detection of sequence variants from miRNA-seq data
  • New Differential Expression methods in sRNAde including Student’s t-test. Visualization of intersection of results with UpsetR.
  • Genome sequences and annotations are automatically derived from Ensembl, including more than 90 species.

11/05/2019: New version of sRNAtoolboxVM

Download it here


Last VM version populate and update are deprecated. Please replace it in /opt/sRNAtoolboxDB/exec/populate and /opt/sRNAtoolboxDB/exec/update with this new ones or download the new version of the VM



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)