Analysis code and results table for a replicate-anchored calibration of intra-host single nucleotide variant detection in Mycobacterium tuberculosis whole genome sequencing
Marie Nancy Séraphin
Open MIND · 2026-01
Abstract
This repository contains the analysis pipeline for calibration of low-frequency variant (iSNV) detection thresholds in short-read whole-genome sequencing of Mycobacterium tuberculosis sputum cultures. Thresholds are anchored using within-patient replicate concordance via a lexicographic selection rule, with bootstrap-based stability assessment. The pipeline applies the calibrated rule to a cohort of patients to estimate per-patient prevalence and longitudinal persistence of within-host diversity.
MeSH terms
- Mycobacterium tuberculosis
- Whole genome sequencing
- Replicate
- Calibration
- Pipeline (software)
- Selection (genetic algorithm)
- Concordance
- Computational biology
- Table (database)
- Biology
- Genotyping
- Tuberculosis
- Single-nucleotide polymorphism
- Inference
- Protocol (science)
- Sputum
- Computer science
- Genetics
- Weighting
- Data mining
- DNA sequencing
- Stability (learning theory)
- Genome