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Km doc updates #1290

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May 24, 2024
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Km doc updates #1290

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7f5830c
update snm3c overview
kayleemathews May 20, 2024
10ec52d
update snm3c overview
kayleemathews May 20, 2024
f881a35
update slide-seq overview
kayleemathews May 20, 2024
2a40435
update docs
kayleemathews May 24, 2024
c567cf4
Update README.md
kayleemathews May 24, 2024
0a3ce1f
Update README.md
kayleemathews May 24, 2024
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Merge branch 'develop' into km_doc_updates
kayleemathews May 24, 2024
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2 changes: 1 addition & 1 deletion website/docs/Pipelines/ATAC/README.md
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| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
| :----: | :---: | :----: | :--------------: |
| [1.2.3](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
| [2.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |


## Introduction to the ATAC workflow
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2 changes: 1 addition & 1 deletion website/docs/Pipelines/Multiome_Pipeline/README.md
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| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
| :----: | :---: | :----: | :--------------: |
| [Multiome v3.4.5](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
| [Multiome v5.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |

![Multiome_diagram](./multiome_diagram.png)

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2 changes: 1 addition & 1 deletion website/docs/Pipelines/Optimus_Pipeline/README.md
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| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
| :----: | :---: | :----: | :--------------: |
| [optimus_v6.6.2](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
| [optimus_v7.1.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |


![Optimus_diagram](Optimus_diagram.png)
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4 changes: 2 additions & 2 deletions website/docs/Pipelines/SlideSeq_Pipeline/README.md
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| Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
| :----: | :---: | :----: | :--------------: |
| [SlideSeq v3.1.5](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:[email protected]) |
| [SlideSeq v3.1.6](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:[email protected]) |

![SlideSeq_diagram](./slide-seq_diagram.png)

## Introduction to the Slide-seq workflow

The [Slide-seq workflow](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/slideseq/SlideSeq.wdl) is an open-source, cloud-optimized pipeline developed in collaboration with the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of spatial transcriptomic data generated with the [Slide-seq](https://www.science.org/doi/10.1126/science.aaw1219) (commercialized as [Curio Seeker](https://curiobioscience.com/product/)) assay.
The [Slide-seq workflow](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/slideseq/SlideSeq.wdl) is an open-source, cloud-optimized pipeline developed in collaboration with the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of spatial transcriptomic data generated with the [Slide-seq](https://www.science.org/doi/10.1126/science.aaw1219) (commercialized as [Curio Seeker](https://curiobioscience.com/seeker/)) assay.

Overall, the workflow corrects bead barcodes, aligns reads to the genome, generates a count matrix, calculates summary metrics for genes, barcodes, and UMIs, returns read outputs in BAM format, and returns counts in numpy matrix and h5ad file formats.

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The Single Nucleus Methly-Seq and Chromatin Capture (snm3C) workflow is an open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics.

The workflow is developed in collaboration with Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker.
The workflow is developed in collaboration with Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker. Please see the [Acknowledgments](#acknowledgements) section below.

For more information about the snm3C tools and analysis, please see the [YAP documentation](https://hq-1.gitbook.io/mc/) or the [cemba_data](https://github.com/lhqing/cemba_data) GitHub repository created by Hanqing Liu.
For more information about the snm3C tools and analysis, please see the [YAP documentation](https://hq-1.gitbook.io/mc/) or the cemba_data GitHub repositories created by [Hanqing Liu](https://github.com/lhqing/cemba_data) and [Wubin Ding](https://github.com/DingWB/cemba_data).

## Quickstart table
The following table provides a quick glance at the Multiome pipeline features:
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