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‎README.md‎

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# snakemake-crispr-guides
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[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0.0-green.svg)](https://snakemake.github.io)
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[![GitHub actions](https://github.com/MPUSP/snakemake-crispr-guides/actions/workflows/main.yml/badge.svg)](https://github.com/MPUSP/snakemake-crispr-guides/actions/workflows/main.yml)
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[![Github Actions](https://github.com/MPUSP/snakemake-crispr-guides/actions/workflows/snakemake-tests.yml/badge.svg)](https://github.com/MPUSP/snakemake-crispr-guides/actions/workflows/snakemake-tests.yml)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1D355C.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-crispr-guides.html)
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The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-crispr-guides.html).
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Detailed information about input data and workflow configuration can also be found in the [`config/README.md`](config/README.md).
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Detailed information about input data and workflow configuration can be found in the [`config/README.md`](config/README.md).
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If you use this workflow in a paper, don't forget to give credits to the author(s) by citing the URL of this (original) repository and its DOI (see above).
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If you use this workflow in a paper, don't forget to give credits to the author(s) by citing the URL of this repository, the release, and its DOI if available.
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## Workflow overview
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### Parameters
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This table lists all parameters that can be used to run the workflow.
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| parameter | type | details | default |
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| ---------------------- | ------- | ---------------------------------------------- | --------------------------------- |
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| GET_GENOME | | | |
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| database | string | one of `ncbi`, `manual` | `ncbi` |
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| assembly | string | RefSeq ID | `GCF_000006945.2` |
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| fasta | path | optional input | `Null` |
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| gff | path | optional input | `Null` |
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| gff_source_type | list | allowed source types in GFF file | `'RefSeq': 'gene', ...` |
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| DESIGN_GUIDES | | | |
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| target_region | numeric | use subset of regions for testing | `["NC_003277.2"]` |
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| target_type | string | specify targets for guide design (see below) | `["target", "intergenic", "ntc"]` |
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| tss_window | numeric | upstream/downstream window around TSS | `[0, 500]` |
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| tiling_window | numeric | window size for intergenic regions | `1000` |
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| tiling_min_dist | numeric | min distance between TSS and intergenic region | `0` |
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| circular | logical | is the genome circular? | `False` |
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| canonical | logical | only canonical PAM sites are included | `True` |
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| strands | string | target `coding`, `template` or `both` | `both` |
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| spacer_length | numeric | desired length of guides | `20` |
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| guide_aligner | string | one of `biostrings`, `bowtie` | `biostrings` |
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| crispr_enzyme | string | CRISPR enzyme ID | `SpCas9` |
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| score_methods | string | see _crisprScore_ package | default scores are listed below |
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| score_weights | numeric | opt. weights when calculating mean score | `[1, 1, 1, 1, 1, 1]` |
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| restriction_sites | string | sequences to omit in entire guide | `Null` |
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| bad_seeds | string | sequences to omit in seed region | `["ACCCA", "ATACT", "TGGAA"]` |
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| no_target_controls | numeric | number of non targeting guides (neg. controls) | 100 |
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| FILTER_GUIDES | | | |
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| filter_best_per_gene | numeric | max number of guides to return per gene | `10` |
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| filter_best_per_tile | numeric | max number of guides to return per ig/tile | `10` |
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| filter_score_threshold | numeric | mean score to use as lower limit | `Null` |
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| filter_multi_targets | logical | remove guides that perfectly match >1 target | `True` |
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| filter_rna | logical | remove guides that target e.g. rRNA or tRNA | `True` |
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| gc_content_range | numeric | range of allowed GC content | `[30, 70]` |
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| fiveprime_linker | string | optionally add 5' linker to each guide | `Null` |
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| threeprime_linker | string | optionally add 3' linker to each guide | `Null` |
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| export_as_gff | logical | export result table to `.gff` file | `True` |
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| export_as_fasta | logical | export result table to `.fasta` file | `True` |
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| REPORT | | | |
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| show_examples | numeric | number of genes to show guide position | `10` |
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| show_genomic_range | numeric | genome start and end pos to show tiling guides | `[0, 50000]` |
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Detailed information about input data and workflow configuration can be found in the [`config/README.md`](config/README.md).
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### Target type
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## Authors
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- The custom `snakemake`, `R`, `R markdown`, and `python` scripts were written by Michael Jahn, PhD
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- Affiliation: [Max-Planck-Unit for the Science of Pathogens](https://www.mpusp.mpg.de/) (MPUSP), Berlin, Germany
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- Visit the MPUSP github page at https://github.com/MPUSP for info on this workflow and other projects
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- Visit the author's github page at https://github.com/m-jahn for info on other projects
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- Dr. Michael Jahn
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- Affiliation: [Max-Planck-Unit for the Science of Pathogens](https://www.mpusp.mpg.de/) (MPUSP), Berlin, Germany
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- ORCID profile: https://orcid.org/0000-0002-3913-153X
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- github page: https://github.com/m-jahn
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## License
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