poursalavati/metaviralyst-datascience repository overview

⁠MetaViralyst Data Science & Reporting Container

This container provides a standardized Python environment for all data processing, aggregation, and report generation steps within the MetaViralyst⁠ virome analysis pipeline.

Using a single, unified container for all scripting rules ensures that Python and library versions (e.g., Pandas, Pysam) are consistent across the entire analysis, guaranteeing reproducibility of data manipulation and statistical calculations.

⁠Pipeline

• Workflow: MetaViralyst
• Version: v1.2+
• Rules: calculate_abundance, filter_contigs, combine_taxonomy, generate_sample_html, generate_summary_html, package_results.

⁠Included Software

This image is built from the mambaorg/micromamba base and includes the following key packages:

• Python: v3.13.7
• Pandas: v2.3.2 - For data manipulation and table I/O.
• Pysam: v0.23.3 - For reading BAM files.
• Jinja2: v3.1.6 - For HTML report templating.
• TaxonKit: v0.20.0 - For taxonomic lineage resolution.
• SeqKit: v2.10.1 - For FASTA/Q sequence manipulation.

⁠🔗 Ecosystem & Related Identifiers

⁠Central Hubs & Applications:

• 🌐 Main Project Website: metaviralyst.ca⁠
• 🖥️ Live Explorer App: app.metaviralyst.ca⁠
• 📊 Benchmark Dashboards: results.metaviralyst.ca⁠

⁠Documentation:

• 📖 Pipeline: pipeline.metaviralyst.ca⁠
• 📖 Explorer: explorer.metaviralyst.ca⁠

⁠Source Code Repositories:

• ⚙️ Pipeline: github.com/poursalavati/MetaViralyst⁠
• 🖥️ Explorer: github.com/poursalavati/MetaViralyst-Explorer⁠

⁠Open Science Archives (Zenodo):

• Ecosystem Source Code Archive (v1.0.0):
• Manuscript Benchmark Results & Demo Data:
• MetaViralyst Custom Viral Databases (v2):
• MetaViralyst Custom Viral Databases (Legacy v1):
• CheckV Reference Database Archive (v1.5):