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Illumina: Very high base accuracy.
Nanopore: Moderate accuracy, error-prone at the base level.
Nanopore/PacBio Duplex: High accuracy, comparable to Illumina. Click again to close
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Advance features, please use Prime editing Analyzer Edit Type:
• Targeted Mutagenesis Oligonucleotide: Uses a repair template to introduce precise changes.
• Prime Editing: Introduces small insertions, deletions, or substitutions.
• Base Editing: Directly converts one base to another.
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More barcode! >> Click to expand
Non-homology end joining KI
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In this field, enter the nuclease target site.
In the Prime Editing Analyzer, this corresponds to the pegRNA.
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Your choice of nuclease enzyme affects the PAM recognition site and the position of the DNA cut relative to the gRNA binding site.
Options for Prime Editing
Advanced options for Prime Editing
These are specified for complexed Prime Editing settings
Optional parameters
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Reference amplicon length should be in the range of 200-300 bases with the nuclease target site located roughly in the middle. You can get the reference from Ensembl link below. Click again to close
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For ONT reads, it is recommended to use -/+15 bases around the predicted DNA lesion. Larger regions are prone to false positive indels. Larger regions (total of 200-250 bp) can be safely used with Illumina reads. You can drag and drop the central point of the predicted double strand break in the genomic sequence to the left or to the right. Default value 0 is double strand breaking point- Edit-o-Matic will use the first index of sgRNA mapped on reference. Click again to close
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The Indel Threshold determines at what relative occurrence an individual indel mutation is considered as a unique allele of the respective clone analyzed, and is thus displayed in the alignment list. Low threshold values can result in false positive allele calling due to sequencing errors, whereas high threshold values result in false negative allele calling. Values in between 0 - 100 % can be entered. We recommend to use 5% for ONT reads and 2% for Illumina reads (default is set to 5%). Click again to close.
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The Quality threshold determine the minimum filter base, For Illumina it should be >20, For ONT it should be >10, Click again to close.
Edit-o-Matic is a JavaScript-based program that was developed for rapid deep sequencing based genotyping of nuclease edited cell clones.
Edit-o-Matic supports noisy Oxford Nanopore but also Next Generation Sequencing (NGS) data such as Illumina and PacBio or Sanger Sequencing.
Edit-o-Matic was developed by Dr. Thach Nguyen in the group of Dr. Andrea Rossi (GEMD lab) at Leibniz Research Institute for Environmental Medicine. The template web interface, data input, output are developed based on the template of Outknocker http://www.outknocker.org/.
Licence:
Edit-o-Matic 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. CRISPRnano 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.
Edit-o-Matic manual
Edit-o-Matic is a JavaScript-based program that was developed for rapid deep sequencing-based genotyping of nuclease edited cell clones. Edit-o-Matic supports noisy Oxford Nanopore but also Next Generation Sequencing (NGS) data such as Illumina, PacBio, or classic Sanger Sequencing.
Detailed manual illustration in the pdf file below
Input data:
Edit-o-Matic webserver analyzes FASTQ output files from ONT, NGS, PacBio or Sanger systems.
It analyzes multiple samples and currently supports up to 96 FASTQ files at the time.
Please(!), make sure that the correct fils order is applied in the file browser.
The file allocation to individual pie charts can be verified by the filename given at alignment track.
Data type:
Dependant on the sequencing datatype, the website will re-update the default parameters optimized for each datatype
Reference sequences, Gene name and gRNA
The reference sequence can be fetched from the genename (GENE SYMBOL in ENSEMBL) automatically. The recommended gRNA will be load when the genename is given.
If you want to use your customized reference, please leave the Gene Name blank.
Nuclease Target Site/gRNA
The Nuclease Target site/gRNA is briefly checked if it is located within the reference genome.
Interested region
For ONT reads, it is recommended to use 90 bp predicted DNA lesion. Larger regions are prone to false positive indels.
Larger regions (total of 100-160 bp) can be safely used with Illumina reads.
Targeting mutagenesis oligonucleotide
Donor oligonucleotide sequence is used to introduce a site-specific genomic modification.
Indel Threshold
The Indel Threshold percentage determines at what relative occurrence an individual indel mutation is considered as a unique allele of the respective clone analyzed, and is thus displayed in the alignment list.
Low threshold values can result in false positive allele calling due to sequencing errors,
whereas high threshold values result in false negative allele calling. Values in between 0 - 100 % can be entered. We recommend using 5% for ONT reads and 2% for Illumina reads (the default is set to 5%).
Current version: 1.6
Released date: 14 th November 2025
Major updates:
- Support cas9/cas12
- Highlight single/double strand breaking point
Previous version: 1.5
Released date: 30th October 2025
Major updates:
- Upgrade to 4 x 96 samples
- Enhanced user interface for better usability
- Added new features/tab for data visualization
Previous version: 1.4
Released date: 17th October 2025
Major updates:
- Different fold change of editing effective (excel/csv files)
Previous version: 1.3
Released date: 20th September 2025
Major updates:
- One time aligner: aligning and storing strategy version ( x 8-12 faster)
Previous version: 1.2
Released date: 17th September 2025
Major updates:
- Applying pair anchors both read and reference version (x 1.5 faster)
Previous version: 1.1
Released date: 3rd September 2025
Major updates:
- Working version of Advance Prime Editing, support preset prefix/suffix RTT, PBS, Desired and Partial Edit
- Quantify Desired/partial edit efficiency
