How jonathan-bravo/telsvirus works
TELSVirus is a Snakemake workflow for detecting viral strains and reconstructing their haplotypes from sequencing reads. The main user-to-result path is read preparation and host/viral alignment, followed by viral-target selection, per-target haplotype reconstruction, and summary output. The repository also includes reference acquisition, duplicate handling, strain annotation, and mapping summaries. The README and selected scripts establish these capabilities, but the Snakefile and rules were not sampled, so workflow wiring is shown only at the documented, high-level orchestration boundary.
Main entry points: Snakefile Snakemake workflow · get_host_ref.smk Host references · get_ref.py Host reference fetch · find_viral_targets.py Viral target selection
Components 23
Workflow control
- Snakemake workflow
workflow/Snakefile
Read processing
- Barcode trimming
workflow/scripts/trim.py - Target alignment
workflow/scripts/align_to_targets.sh - Host references
workflow/rules/get_host_ref.smk - Host reference fetch
workflow/scripts/get_ref.py
Viral analysis
- Viral target selection
workflow/scripts/find_viral_targets.py - Duplicate detection
workflow/scripts/find_duplicates.py - Read clustering
workflow/scripts/cluster_reads.py - BLAT alignment
workflow/scripts/run_blat.py - Read deduplication
workflow/scripts/deduplicate.py - RVHaplo preflight
workflow/scripts/rvhaplo_preflight.py - Haplotype reconstruction
RVHaplo
References and results
- Haplotype parsing
workflow/scripts/parse_rvhaplo.py - Strain database
- Strain database rules
workflow/rules/strain_db.smk - Strain database generator
workflow/scripts/gen_strain_source_db.py - Viral segment annotation
workflow/scripts/add_viral_segments.py - Mapping summaries
workflow/scripts/summarize_idxstats.py
Other components
- Analyst
- NCBI RefSeq
- NCBI Entrez
- BLAT
- Sequencing reads
Connections 22
- Analyst → Snakemake workflow: runs
- Sequencing reads → Snakemake workflow: provides reads
- Snakemake workflow → Barcode trimming: dispatches
- Snakemake workflow → Host references: dispatches
- Snakemake workflow → Viral target selection: dispatches
- Snakemake workflow → Duplicate detection: dispatches
- Snakemake workflow → Read clustering: dispatches
- Snakemake workflow → Read deduplication: dispatches
- Snakemake workflow → RVHaplo preflight: dispatches
- Snakemake workflow → Haplotype reconstruction: dispatches
- Snakemake workflow → Haplotype parsing: dispatches
- Snakemake workflow → Strain database rules: dispatches
- Snakemake workflow → Viral segment annotation: dispatches
- Snakemake workflow → Mapping summaries: dispatches
- Host references → Host reference fetch: invokes
- Host reference fetch → NCBI RefSeq: downloads genome
- BLAT alignment → BLAT: invokes
- Viral segment annotation → NCBI Entrez: fetches metadata
- Strain database rules → Strain database generator: invokes
- Viral target selection → Strain database: reads names
- Haplotype parsing → Strain database: reads names
- Mapping summaries → Strain database: reads names