PiGx
PiGx (Pipelines in Genomics) is a suite of reproducible and user-friendly genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples. Designed to streamline the analysis of high-throughput sequencing data, PiGx offers several specialized pipelines:
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PiGx BSseq: Processes raw FASTQ files from bisulfite sequencing experiments to analyze DNA methylation patterns.
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PiGx RNAseq: Handles RNA sequencing data, providing comprehensive analyses including differential expression and quality control.
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PiGx scRNAseq: Caters to single-cell RNA sequencing data, offering preprocessing, quality control, and downstream analyses.
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PiGx ChIPseq: Analyzes ChIP sequencing data, performing tasks such as peak calling and generating detailed reports.
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PiGx CRISPR: (In development) Aims to analyze sequence mutations in CRISPR-Cas9 targeted amplicon sequencing data.
Each pipeline is configured using a simple sample sheet and a descriptive settings file, resulting in interactive HTML reports that summarize key findings. PiGx is distributed through GNU Guix, ensuring reproducibility and ease of installation. The source code is available under the GNU General Public License, inviting community contributions.