[meta]
name = "pbfusion"
category = "rna-seq"
description = "PacBio's RNA fusion gene detector for long-read IsoSeq data"
tags = ["rna-seq", "fusion", "pacbio", "isoseq", "long-read", "transcript", "cancer"]
author = "oxo-call built-in"
source_url = "https://github.com/PacificBiosciences/pbfusion"

[context]
concepts = [
    "pbfusion detects gene fusions from PacBio IsoSeq full-length RNA-seq data.",
    "Input: aligned IsoSeq BAM (aligned with pbmm2 using ISOSEQ preset) and a GTF annotation.",
    "pbfusion uses full-length read coverage to detect fusion breakpoints with base-pair resolution.",
    "Requires sorted, indexed, aligned IsoSeq BAM from pbmm2 --preset ISOSEQ.",
    "Output: fusions.tsv with fusion gene pairs, breakpoints, and supporting read counts.",
    "Long-read fusions are more precise than short-read fusions (full spanning reads).",
    "Use --threads for parallel processing; --output-dir for results.",
]

pitfalls = [
    "pbfusion requires IsoSeq data, not regular RNA-seq — it needs full-length transcripts.",
    "Input BAM must be aligned with IsoSeq-specific parameters (pbmm2 --preset ISOSEQ).",
    "pbfusion requires a Gencode or Ensembl GTF annotation file.",
    "Low-coverage fusions may be missed — deeper IsoSeq sequencing improves sensitivity.",
]

[[examples]]
task = "detect gene fusions from PacBio IsoSeq aligned data"
args = "--bam isoseq_aligned.bam --gtf genes.gtf --output-dir fusion_output/ --threads 8"
explanation = "--bam aligned IsoSeq BAM; --gtf gene annotation; --output-dir for results"

[[examples]]
task = "detect fusions with minimum supporting reads"
args = "--bam isoseq_aligned.bam --gtf genes.gtf --output-dir fusion_output/ --min-support 3 --threads 8"
explanation = "--min-support 3 requires at least 3 reads supporting each fusion; reduces false positives"
