https://github.com/pinellolab/crispresso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
https://github.com/pinellolab/crispresso2

amplicon-sequences genome-editing quantification

Last synced: 27 days ago
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Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

• Host: GitHub
• URL: https://github.com/pinellolab/crispresso2
• Owner: pinellolab
• License: other
• Created: 2018-05-14T20:01:18.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2026-04-23T20:08:56.000Z (27 days ago)
• Last Synced: 2026-04-23T21:29:19.104Z (27 days ago)
• Topics: amplicon-sequences, genome-editing, quantification
• Language: Python
• Homepage:
• Size: 3.51 MB
• Stars: 336
• Watchers: 14
• Forks: 115
• Open Issues: 58
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.txt

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# CRISPResso2

CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. A limited web implementation is available at: https://crispresso2.pinellolab.org/.

Briefly, CRISPResso2:

- aligns sequencing reads to a reference sequence

- quantifies insertions, mutations and deletions to determine whether a read is modified or unmodified by genome editing

- summarizes editing results in intuitive plots and datasets

Access the full documentation at .

In addition, CRISPResso can be run as part of a larger tool suite:

- [CRISPRessoBatch](https://docs.crispresso.com/suite/batch/tool.html) - for analyzing and comparing multiple experimental conditions at the same site

- [CRISPRessoPooled](https://docs.crispresso.com/suite/pooled/tool.html) - for analyzing multiple amplicons from a pooled amplicon sequencing experiment

- [CRISPRessoWGS](https://docs.crispresso.com/suite/wgs/tool.html) - for analyzing specific sites in whole-genome sequencing samples

- [CRISPRessoCompare](https://docs.crispresso.com/suite/compare/tool.html) - for comparing editing between two samples (e.g., treated vs control)

- [CRISPRessoAggregate](https://docs.crispresso.com/suite/aggregate/tool.html) - for aggregating results from previously-run CRISPResso analyses

![CRISPResso2 Schematic](https://raw.githubusercontent.com/pinellolab/CRISPResso2/master/crispresso_schematic.png "CRISPResso2 Schematic")

## Installation

CRISPResso2 can be [installed](https://docs.crispresso.com/installation.html) in the following ways:

- [Bioconda](https://docs.crispresso.com/installation.html#bioconda)

  - [Bioconda on Apple Silicon](https://docs.crispresso.com/installation.html#bioconda-for-apple-silicon)

- [Docker](https://docs.crispresso.com/installation.html#docker)

## Examples

- [CRISPResso example runs](https://docs.crispresso.com/suite/core/examples.html)

- [CRISPRessoBatch example runs](https://docs.crispresso.com/suite/batch/examples.html)

- [CRISPRessoPooled example runs](https://docs.crispresso.com/suite/pooled/examples.html)

- [CRISPRessoWGS example runs](https://docs.crispresso.com/suite/wgs/examples.html)

- [CRISPRessoCompare example runs](https://docs.crispresso.com/suite/compare/examples.html)

- [CRISPRessoPooledWGCompare example runs](https://docs.crispresso.com/suite/pooledwgscompare/examples.html)

- [CRISPRessoAggregate example runs](https://docs.crispresso.com/suite/aggregate/examples.html)

## Troubleshooting

If you run into any issues, check out the [Troubleshooting page](https://docs.crispresso.com/troubleshooting.html) or submit a [new discussion](https://github.com/pinellolab/CRISPResso2/discussions/new?category=troubleshooting).