Welcome to the download page of decontaMiner, a tool for detecting contaminating organisms in human unmapped sequences.

Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level.

Nonetheless, a variable number of reads fails to correctly align to the reference. In most of the cases this failure is due to the low quality of the bases called during the sequencing, but very often this 'misalignment' is due to sequence differences between the reads and the corresponding genome.

Investigating the source of these reads is definitely important to better assess the quality of the whole experiment, and to look for possible downstream or upstream 'contamination' from exogenous nucleic acids.

DecontaMiner is a tool designed and developed for the detection and analysis of these contaminating sequences. DecontaMiner is aimed at help researchers in obtaining more information from the data, and, in particular, to check for microorganisms presence that can not only affect the reliability of the whole experiment, but also foster the evaluation of the samples and the conditions under an additional perspective.


The download area below provides access to the following items:

  • the current version of DecontaMiner code
  • the installation and user guide
  • the test data (please be patient, it is aboout 1.2 GB of data: the download may take some time)

An example of the interactive html report generated by DecontaMiner on the test data is available HERE.

decontaMiner at a glance

Download area

  • tar.gz decontaminer.tar.gz Tar gzipped archive of the decontaminer software
  •  pdf   InstallationAndUserGuide.pdf Decontaminer installation and user guide
  • tar.gz test_data.tar.gz Tar gzipped archive of the single-end unmapped bam test data

    Databases of contaminating organisms (please be patient, databases size is large.)

  • .zip VIRUSES_db.zip zipped archive of the viruses database
  • .zip Human_rna.zip zipped archive of the human RNA database
  • .zip FUNGI_db.zip zipped archive of the fungi database
  • .zip BACTERIA_db.zip zipped archive of the fungi database

Upload your Results

barplotinfo* file : (Examplefile)