DeconSeq. DECONtamination of SEQuence data.

Detect and remove contaminations
from your sequence data.

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

Input interface

The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes.

Interactive threshold selection

The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats.

Coverage-Identity plots

The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

News and Updates

Here you will find release notes and news related to DeconSeq.

05 / 2013

Release of version 0.4.3: Fixed issue when multiple chunks per database were specified in the config file that did not correctly split during search. (Thanks to Osvaldo Zagordi for pointing out the problem.)

03 / 2013

Release of version 0.4.2: Added FindBin module to find config file when run from outside the source directory. Improve readme file. Allow multiple chunks per database to be specified in the config file and used with a single database name in -dbs.

09 / 2011

Release of version 0.4.1: Fixed issue with missing method generateFastaFromIds. (Thanks to Valmik Desai for pointing out the problem.) Extended the input format from ACGTN to full nucleic acid ambiguity code (ACGTURYKMSWBDHVNX-).

07 / 2011

Release of version 0.4: Added FASTQ support to standalone version.

04 / 2011

Release of version 0.3.2: Removed debugging print out (3). Fixed issues of undefined output during FASTA file generation and grouping when using option dbs_retain.

02 / 2011

Release of version 0.3: Updated BWA-SW from 0.5.8 to 0.5.9 (bugfix of very rare mismappings and change of scoring matrix, see for more details).

11 / 2010

DeconSeq web version update with fix for FASTQ output issue and user convenient naming of output files.

09 / 2010

DeconSeq release 0.2 including small fixes, code cleanup, and the modified version of BWA-SW.

08 / 2010

We added new databases to the web version: 18S rRNA, mouse, zebrafish, mosquitoes, archaea

Updates of the bacterial and viral databases.

07 / 2010

The DeconSeq web version goes online.