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. Thus, the workflow goes through the following steps:
- FASTQ sequencing Quality Control through FastQC
- Mapping FASTQ against a reference genome throught BWA
- Sorting, Deduplicating and Indexing of BAM files through Samtools & sambaba
- Generating features and use ashleys-qc model to identify high-quality cells
📚 Homepage: https://friendsofstrandseq.github.io/mosaicatcher-docs/
- Ebert Peter
- Grimes Karen
- Gros Christina
- Korbel Jan
- Marschall Tobias
- Sanders Ashley
- Weber Thomas (maintainer and current developer)
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.