miRTrace

miRTrace is an algorithm that identifies the taxonomic origins of microRNA sequencing data. This capability is crucial across various fields, including forensics, parasitology, food control, and scientific research, where cross-contamination may impact the integrity of results. miRTrace demonstrates exceptional accuracy, over 99%, in categorizing actual and simulated data into 14 significant animal and plant groups. It is highly sensitive in detecting parasitic infections in mammals and can even pinpoint the primate origin of single cells. An analysis of more than 700 public datasets using miRTrace revealed that over 7% suffer from cross-contamination. miRTrace offers a novel computational method to clean these datasets post-sequencing. The tool is available for free at https://github.com/friedlanderlab/mirtrace.

Topic

Functional, regulatory and non-coding RNA;RNA-seq;Parasitology

Detail

  • Operation: Sequence trimming;miRNA target prediction;miRNA expression analysis

  • Software interface: Command-line interface

  • Language: Java

  • License: The GNU General Public License v3.0

  • Cost: Free with restrictions

  • Version name: -

  • Credit: The Strategic Research Area (SFO) program of the Swedish Research Council (VR) through Stockholm University.

  • Input: -

  • Output: -

  • Contact: Marc R. Friedländer marc.friedlander@scilifelab.se

  • Collection: -

  • Maturity: Stable

Publications

  • miRTrace reveals the organismal origins of microRNA sequencing data.
  • Kang W, et al. miRTrace reveals the organismal origins of microRNA sequencing data. miRTrace reveals the organismal origins of microRNA sequencing data. 2018; 19:213. doi: 10.1186/s13059-018-1588-9
  • https://doi.org/10.1186/s13059-018-1588-9
  • PMID: 30514392
  • PMC: PMC6280396

Download and documentation

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