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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:\n\n1. FASTQ sequencing Quality Control through [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n2. Mapping FASTQ against a reference genome throught [BWA](http://bio-bwa.sourceforge.net/)\n3. Sorting, Deduplicating and Indexing of BAM files through [Samtools](http://www.htslib.org/) \u0026 [sambaba](https://lomereiter.github.io/sambamba/docs/sambamba-view.html)\n4. Generating features and use [ashleys-qc](https://github.com/friendsofstrandseq/ashleys-qc) model to identify high-quality cells\n\n## Documentation\n\n**📚 Homepage:** [https://friendsofstrandseq.github.io/mosaicatcher-docs/](https://friendsofstrandseq.github.io/mosaicatcher-docs/)\n\n## Authors (alphabetical order)\n\n- Ebert Peter\n- Grimes Karen\n- Gros Christina\n- Korbel Jan\n- Marschall Tobias\n- Sanders Ashley\n- Weber Thomas (maintainer and current developer)\n\n## References\n\n\u003e 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.\n\n\u003e 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffriendsofstrandseq%2Fashleys-qc-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffriendsofstrandseq%2Fashleys-qc-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffriendsofstrandseq%2Fashleys-qc-pipeline/lists"}