OutKnocker Try OutKnocker 2.0 beta today!

Gene Name (optional): (?)

Reference Sequence: (?)

Nuclease Target Site: (?)

Indel Threshold [%]: (?)

Phred Score Threshold: (?)

Targeting mutagenesis oligonucleotide (optional), [highlighted region] (optional): (?)

FASTQ Files: (?) (example file)


OutKnocker is a javascript-based program that was developed for rapid deep sequencing based genotyping of nuclease edited cell clones. OutKnocker was developed by J. Schmid-Burgk and T. Schmidt and coded by J. Schmid-Burgk in the group of Veit Hornung at Institute of Molecular Medicine, University Hospital, University of Bonn.

The following example FASTQ file can be downloaded by right klicking: example file. In this example, the human BIRC3 gene was targeted by CRISPR/Cas9 genome editing. The corresponding amplicon and target site sequences are entered above per default.


Veit Hornung
Institute of Molecular Medicine
University Hospital Bonn
Sigmund-Freud-Str. 25
53127 Bonn, Germany


OutKnocker was successfully tested on:
  • Mozilla Firefox version 47.0
  • Google Chrome version 35.0
  • Opera version 20.0


    OutKnocker can be redistributed and/or modified under the terms of the GNU General Public License (Version 2), as published by the Free Software Foundation. A copy of the license can be found online at www.gnu.org/licenses. OutKnocker is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

    Citing OutKnocker:

    We kindly request that use of this software be cited in publications as:
    Jonathan L. Schmid-Burgk, Tobias Schmidt, Moritz M. Gaidt, Karin Pelka, Eicke Latz, Thomas S. Ebert, and Veit Hornung. Genome Research 2014

    Version history:

    Outknocker V1.31 (07/2016)
    - Sequence logo is shown also for failed alignment reads

    Outknocker V1.3 (06/2016)
    - Navigation menu
    - A mutation statistics table can be generated allowing to assess polyclonal genome editing
    - Print / save as PDF
    - Small pie charts are clickable

    Outknocker V1.2 (06/2015)
    - Memory use is fixed to roughly 200 MB, sequence alignment visualization is always enabled
    - Mutation threshold for pie charts is fixed to 0.1% for better visualization of sequencing quality

    Outknocker V1.1 (05/2015)
    - Large files >1 GB can be analyzed
    - Pie charts and alignments can be saved as SVG images
    - Minor bases are included in the alignment sequence logo
    - Small letters are allowed in the reference sequence and target site. Antisense target site sequences are allowed.

    Outknocker V1.0 (07/2014)
    - Public release of OutKnocker.org

    Privacy Policy:

    The following data protection declaration applies to the use of our online offer OutKnocker.org (hereinafter "Website"). We attach great importance to data protection. Your personal data is collected and processed in compliance with the applicable data protection regulations, in particular the General Data Protection Regulation (GDPR). We collect and process your personal data in order to be able to offer you the above-mentioned portal. This statement describes how and for what purpose your data is collected and used and what options you have in connection with personal data. By using this website, you consent to the collection, use and transfer of your information in accordance with this Privacy Policy. 1 Responsibility Responsible for the collection, processing and use of your personal data within the meaning of Art. 4 No. 7 DSGVO is Jonathan Schmid-Burgk, Goebenstr. 28, 53113 Bonn, Germany, jonathan@synleor.com If you wish to object to the collection, processing or use of your data by us in accordance with these data protection regulations as a whole or for individual measures, you can address your objection to the entity responsible. You can save and print this data protection declaration at any time. 2 General website usage 2.1 Hosting The hosting services we use serve to provide the following services: Infrastructure and platform services, computing capacity, storage and database services, security services and technical maintenance services that we use to operate the Site. We or our hosting provider process inventory data, content data, usage data, meta- and communication data of customers, interested parties and visitors of this online offer on the basis of our legitimate interests in an efficient and secure provision of this online offer according to Art. 6 Para. 1 S. 1 f) DSGVO in connection with Art. 28 DSBER. 2.2 Access data We collect information about you when you use this website. We automatically collect information about your usage behavior and interaction with us and record data about your computer or mobile device. We collect, store and use data about every access to our online offer (so-called server log files). 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