Metadata-Version: 2.4
Name: CRISPResso2
Version: 2.3.4
Summary: Software pipeline for the analysis of genome editing outcomes from deep sequencing data
Author-email: "Edilytics, Inc." <support@edilytics.com>
Project-URL: Homepage, https://github.com/pinellolab/CRISPResso2
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: Other/Proprietary License
Classifier: Operating System :: POSIX
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Cython
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: jinja2
Requires-Dist: scipy
Requires-Dist: numpy
Provides-Extra: dev
Requires-Dist: cython; extra == "dev"
Dynamic: license-file

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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 <https://docs.crispresso.com>.

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).
