bio-workflows-longread-sv-pipeline

name	bio-workflows-longread-sv-pipeline
description	Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.
tool_type	cli
primary_tool	Sniffles
workflow	true
depends_on	["long-read-sequencing/basecalling","long-read-sequencing/long-read-alignment","long-read-sequencing/long-read-qc","long-read-sequencing/structural-variants"]
qc_checkpoints	[{"after_qc":"Read N50 >10kb, mean quality >Q10 (ONT R10) / HiFi rq>0.99"},{"after_alignment":"Mapping rate >90%, coverage >=15x for confident SV calling"},{"after_calling":"SV count in the expected range, INS/DEL ratio sane, genotypes concordant"},{"after_benchmark":"Truvari F1 reported WITH its refdist/pctsize/pctseq, on Tier 1 AND CMRG"}]

Version Compatibility

Reference examples tested with: minimap2 2.28+, Sniffles 2.2+, cuteSV 2.1+, pbsv 2.9+, dipcall 0.3+, bcftools 1.19+, samtools 1.19+, truvari 4.0+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

Use minimap2 >= 2.28: the lr:hq accurate-read preset was added in 2.27, and 2.28 fixes the 2.27 --MD regression. Supply a reference-matched tandem-repeat BED to the caller - it is the single biggest false-positive lever in repeats. Truvari renamed the alt-sequence-similarity param from --pctsim to --pctseq at v4; confirm against truvari bench --help.

If code throws an error, introspect the installed tool and adapt the example to the actual API rather than retrying.

Long-Read SV Pipeline

"Detect structural variants from my long-read sequencing data" -> Chain basecalling, platform-matched minimap2 alignment, an SV caller selected by platform and goal, an optional assembly-based branch, cohort merging, and a parameterized Truvari benchmark - with the SV mechanism delegated to the component skills.

This is a workflow (orchestration) skill: it makes the stage-to-stage decisions and quality gates that connect the component skills. It does NOT re-teach how a caller sees an SV or the VCF representation minefield - that lives in variant-calling/structural-variant-calling and long-read-sequencing/structural-variants.

Why long reads for SV: the physics that justifies this pipeline

Run this pipeline instead of a short-read SV workflow for one mechanistic reason: a single long read (PacBio HiFi ~15-25 kb, ONT tens of kb to >Mb ultralong) physically spans the SV and both flanks in one molecule, turning SV detection from an inference-over-fragments problem into near-direct observation. Two consequences decide whether long reads earn their per-sample cost:

• Insertions become tractable. Placing and sizing an insertion needs reads that carry the novel bases; when an INS exceeds Illumina read length (150 bp) no short read spans it, so short-read INS recall is stuck at ~30-50% while long reads reach ~90%+. Ebert 2021 (Science 372:eabf7117) found 68% of 107,590 assembly-discovered SVs were missed by short reads. If insertions matter, this pipeline is the answer, not a tuning knob.
• Repeat-mediated junctions resolve. A 20 kb read anchored in unique sequence on both flanks spans a breakpoint buried in a 5 kb repeat that no 150 bp read can straddle, bringing segmental-duplication NAHR, mobile-element insertions, and VNTR/STR expansions into reach.

The governing pipeline principle: an SV call is a of choices made upstream. The aligner preset, the tandem-repeat BED handed to the caller, and the Truvari matching parameters move precision/recall as much as the caller does. Chaining decisions - not the caller name - are what this skill is about.