Methods That Produce Reviewable Evidence

GeneFlow standardizes computational steps and preserves their outputs. The software surfaces evidence; qualified researchers remain responsible for interpretation.

Reference Context & AB1 QC

Pipeline definitions record rCRS or RSRS context. For AB1 data, GeneFlow extracts base calls, Phred scores, and four-channel traces, then computes consistent screening signals for researcher review.

  • Explicit rCRS or RSRS pipeline context
  • Automated Phred distributions and quality flags
  • Detected low-quality regions
  • Suggested, not enforced, trim boundaries
COMPUTATION + EXPERT REVIEW

Haplogroup Evidence Review

HaploGrep3 produces a classification, quality value, and mutation evidence. GeneFlow can compare that output with a recorded MitoMaster result and keeps disagreements open for expert resolution.

  • Per-tool calls, quality, and status
  • Found-mutation evidence
  • Visible match or conflict state
  • Named resolution with notes and history

Phylogenetic Inference

GeneFlow aligns project sequences with MAFFT and infers a tree with FastTree. The resulting Newick topology is an analytical output to examine alongside sampling context, not a substitute for population-genetic interpretation.

  • MAFFT multiple-sequence alignment
  • FastTree tree inference
  • Newick output with tip labels
  • Method, sequence count, and run status

Evidence-Centered Reporting

Generate sample or project reports from the evidence already held in GeneFlow. Reports communicate computed results and documented review; they do not convert analytical output into an expert conclusion.

  • Sample-level or project-wide scope
  • Structured QC and haplogroup tables
  • Pipeline-run linkage where applicable
  • Downloadable PDF artifacts