https://github.com/friendsofstrandseq/ashleys-qc-pipeline

Strand-Seq Quality Control Pipeline based on ashleys-qc
https://github.com/friendsofstrandseq/ashleys-qc-pipeline

bioinformatics genomics pipeline preprocessing quality-control sequencing snakemake strand-seq

Last synced: 5 months ago
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Strand-Seq Quality Control Pipeline based on ashleys-qc

• Host: GitHub
• URL: https://github.com/friendsofstrandseq/ashleys-qc-pipeline
• Owner: friendsofstrandseq
• License: mit
• Created: 2020-11-17T16:33:29.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2025-07-08T21:53:01.000Z (12 months ago)
• Last Synced: 2025-07-08T22:33:32.269Z (12 months ago)
• Topics: bioinformatics, genomics, pipeline, preprocessing, quality-control, sequencing, snakemake, strand-seq
• Language: Jupyter Notebook
• Homepage:
• Size: 2.5 MB
• Stars: 4
• Watchers: 3
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
![logo](docs/images/logo.png)

[![Workflow checks](https://github.com/friendsofstrandseq/ashleys-qc-pipeline/actions/workflows/main_test.yaml/badge.svg)](https://github.com/friendsofstrandseq/ashleys-qc-pipeline/actions/workflows/main_test.yaml)

[![Snakemake](https://img.shields.io/badge/snakemake-≥7.12.0-brightgreen.svg)](https://snakemake.github.io)

# ashleys-qc-pipeline

ashleys-qc-pipeline performs Quality Control analysis on Strand-Seq single-cell

sequencing data. The starting point are single-cell FASTQ files from Strand-seq experiments and the final output produced is a folder with clean selected BAM files. The pipeline can identify automatically high-quality libraries through ML-based analysis tool [ashleys-qc](https://github.com/friendsofstrandseq/ashleys-qc). Thus, the workflow goes through the following steps:

1. FASTQ sequencing Quality Control through [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

2. Mapping FASTQ against a reference genome throught [BWA](http://bio-bwa.sourceforge.net/)

3. Sorting, Deduplicating and Indexing of BAM files through [Samtools](http://www.htslib.org/) & [sambaba](https://lomereiter.github.io/sambamba/docs/sambamba-view.html)

4. Generating features and use [ashleys-qc](https://github.com/friendsofstrandseq/ashleys-qc) model to identify high-quality cells

## Documentation

**📚 Homepage:** [https://friendsofstrandseq.github.io/mosaicatcher-docs/](https://friendsofstrandseq.github.io/mosaicatcher-docs/)

## Authors (alphabetical order)

- Ebert Peter

- Grimes Karen

- Gros Christina

- Korbel Jan

- Marschall Tobias

- Sanders Ashley

- Weber Thomas (maintainer and current developer)

## References

> MosaiCatcher v2 publication: Weber Thomas, Marco Raffaele Cosenza, and Jan Korbel. 2023. ‘MosaiCatcher v2: A Single-Cell Structural Variations Detection and Analysis Reference Framework Based on Strand-Seq’. Bioinformatics 39 (11): btad633. https://doi.org/10.1093/bioinformatics/btad633.

> Gros, Christina, Ashley D Sanders, Jan O Korbel, Tobias Marschall, and Peter Ebert. “ASHLEYS: Automated Quality Control for Single-Cell Strand-Seq Data.” Bioinformatics 37, no. 19 (October 1, 2021): 3356–57. https://doi.org/10.1093/bioinformatics/btab221.