Decontaminer tool : detecting unexpected contamination in unmapped NGS data

Our decontaminer web server is under maintenance, so we are making it available here. Please read the decontaminer publication for more details.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x

Compressed folder "decontaMiner_1.4.tar.gz" contains latest version of the tool. Required databases can be downloaded from link mentioned below.

DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. DecontaMiner builds an offline HTML page containing summary statistics and plots. The software is freely available at http://www-labgtp.na.icar.cnr.it/decontaminer.

Three Main scripts to Run

Step 1 :     (a) decontaMiner.sh

Step 2 :     (b) filterBlastInfo.sh and

Step 3 :     (c) collectInfo.sh

Database download link (Pre built)

https://drive.google.com/drive/u/2/folders/1UQCiuUVnS5TpkT0We2AkRVew-km_gR_u

R script for o/p visualization

Please find the code here https://rpubs.com/amarinder1/deontaminer or https://github.com/amarinderthind/decontaminer/tree/master/R_decontaminer_visualizationScript

some updates for database configration settings

if you have fasta and idx path as listed below

    fasta path     DB/HUMAN_RNA/rRNA.fasta

    idx path     DB/HUMAN_RNA/rRNA.idx

You should mention this in configuration file in the following way

RIBO_DB=DB/HUMAN_RNA
RIBO_NAME=rRNA

Download link for example BAM files

https://drive.google.com/drive/u/2/folders/1B9WNJc1cGY_LIi2XGwkQ0h_9916_A8Ij

Updates on Paired end reads error

Decontaminer expects the following Paired end reads format:

@A00121:137:HTLF3DSXX:3:1110:3097:35571/1
@A00121:137:HTLF3DSXX:3:1110:3097:35571/2

If you have other reads format (like below) format of PR reads, you can rename/change from

@A00121:137:HTLF3DSXX:3:1110:3097:35571 0:N: 00
@A00121:137:HTLF3DSXX:3:1110:3097:35571 1:N: 00

To following using simple linux command (mentioned below), with this command it will be converted to the required format like below:

@A00121:137:HTLF3DSXX:3:1110:3097:35571/1
@A00121:137:HTLF3DSXX:3:1110:3097:35571/2

Here is an example of Linux command

sed 's/ 0:N:0://1/g' inputfile > outputfile
sed 's/ 1:N:0://2/g' inputfile > outputfile

Flow Chart of the Pipeline

Overview of the results Visualization