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TruePure – Contamination Analysis for Sequencing

TruePure provides a fast mechanism to check for contamination in NGS sequence files. In order to provide a fast answer files up to 10,000 reads are allowed.

To use TruePure, you will need sequences. You can use those sequences that were directly given by the Next Generation Sequencing instrument or sequences processed by you. The format in which the sequences should be is fastq or fasta – TruePure does not use the quality information in the fastq file. For a contamination analysis, it is sufficient to analyze 10,000 random reads, so it will not take long to upload those reads to our server, but of course this will depend on the speed of your upload.

Important: This tool is not restricted to human samples!

The Results

  • The csv file
  • The pdf file

In the csv file you will have all species found in your file with the number of reads that were aligned to those species. For our example file, you get the following result:

 V1  V2  V3
 Species name  Not_found  Mycoplasma hyorhinis  Spirometra erinaceieuropaei
 Species number (uniport)  0  2100  99802
 Number of sequences found  0  9  1
 The composition of species
Mycoplasma hyorhornis
Spirometra erinaceieuropaei

The pdf file contains a circular bar chart of the mixture of your sequences. All species with more sequences than 5% of all sequences will get an individual color and name, all others are summarized in “other”,  but are detailed in the csv file with actual numbers. The percentage of contamination is also noted, but calculated for the species with the highest occurrence, which may not be the species you wanted!

User Instructions:

Check this guide for more information

How to Use this Tool:

  • Please extract 10,000 reads from your file (nucleotide sequences of course). If you do not know how to extract 10,000 reads, please use the extraction tool
  • Choose the file type for your data
  • Upload your (max) 10,000 reads file (less is of course possible), enter your email address and start the tool
  • You will receive an email with a link to your results after the tool is finished
  • We will delete your files after 3 to 7 days, depending on the usage of our tools.