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msianalyzer

https://github.com/nagellabhub/msianalyzer

Science Score: 57.0%

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Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: NagelLabHub
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 3.79 MB
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  • Stars: 1
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Created about 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

MSIanalyzer

MSIanalyzer is a flexible pipeline for high-resolution analysis and visualization of Microsatellite Instability (MSI) and tandem repeat regions from sequencing reads.

Key Features

  • Universal Repeat Region Analysis – Supports user-defined primers targeting any repetitive motif region.
  • Per-Read Repeat Count Quantification – High-resolution repeat unit counting for accurate MSI profiling.
  • Detailed Indel Characterization – Precise detection and annotation of interruptions in repeat sequences.
  • Customized Pileup Visualizations – Clear visual summaries of coverage, repeats, indels, and genomic context.
  • Optimized for Nanopore Data – Designed to tolerate higher error rates and fully leverage ONT long-read sequencing.
  • Cluster-Aware Statistical Analysis – Incorporates read clustering to enhance detection of sample-level differences.

Installation

bash pip install git+https://github.com/NagelLabHub/MSIanalyzer.git

Quick Usage Example

A ready-to-run Google Colab notebook is available here to demonstrate an example run of MSIanalyzer using the built-in example data.

To run MSIanalyzer via the command line, use the following examples from the example folder:

```bash

Run analysis on a single marker (without or with sample comparison)

msianalyzer run-marker BAT25 examplemarker.json msianalyzer run-marker BAT25 examplemarker.json --run-tests

Run batch analysis on all markers in the JSON (can use '--threads' for parrallel processing)

msianalyzer run-batch example_marker.json

Generate pileup visualization for FASTQ file(s)

msianalyzer pileup fastqexample/BVSBWG3500x.fastq hg38/chr4BAT25.fa ```

Citation

If you use this software, please cite:

Ting Zhai, Daniel J. Laverty, Zachary D. Nagel (2025). MSIanalyzer: Targeted Nanopore Sequencing Enables Single Nucleotide Resolution Analysis of Microsatellite Instability Diversity. bioRxiv 2025.06.26.661510. https://doi.org/10.1101/2025.06.26.661510

Owner

  • Name: Nagel Lab
  • Login: NagelLabHub
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it using the metadata below."
title: "MSIanalyzer: Targeted Nanopore Sequencing Enables Single Nucleotide Resolution Analysis of Microsatellite Instability Diversity"
authors:
  - family-names: Zhai
    given-names: Ting
    email: tingzhai@hsph.harvard.edu
    affiliation: Harvard T.H. Chan School of Public Health
  - family-names: Laverty
    given-names: Daniel J.
    affiliation: Harvard T.H. Chan School of Public Health
  - family-names: Nagel
    given-names: Zachary D.
    affiliation: Harvard T.H. Chan School of Public Health
abstract: "We present a targeted sequencing-based pipeline that profiles microsatellite instability (MSI) at single-nucleotide resolution. Targeted amplicons from the five widely studied Bethesda panel microsatellite loci were sequenced using Oxford Nanopore Technology in two microsatellite unstable colorectal cancer cell lines (HCT15, HCT116), two microsatellite stable cancer cell lines (TK6, U2OS), and two peripheral blood mononuclear cell samples from healthy donors. An anchor-extension algorithm was developed to capture repeat motifs while allowing interruptions, using a threshold informed by platform-specific error. Cluster-aware Dirichlet-multinomial and beta-binomial tests were applied for between-sample comparisons while accounting for read-level clustering within samples. The algorithm revealed distinct repeat profiles in HCT15 and HCT116 compared to other cell types and uncovered allelic diversity across samples at different MSI loci. Our approach complements existing short tandem repeat callers by preserving read-level diversity and delivering targeted, quantitative MSI calls with potential applications in mechanistic research and clinical assay development."
keywords:
  - microsatellite instability
  - nanopore sequencing
  - single nucleotide resolution
  - MSI
  - colorectal cancer
  - bioinformatics
type: software
date-released: 2025-06-28
version: "1.0.0"
license: MIT
repository-code: https://github.com/NagelLabHub/msianalyzer
url: https://www.biorxiv.org/content/10.1101/2025.06.26.661510v1
doi: 10.1101/2025.06.26.661510

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Dependencies

pyproject.toml pypi
  • adjustText >=1.0
  • biopython >=1.83
  • joblib >=1.4
  • matplotlib >=3.9
  • numpy >=2.0
  • pandas >=2.2
  • pyarrow >=14
  • pysam >=0.22
  • python-Levenshtein >=0.25
  • scikit-bio >=0.6.3
  • scikit-learn >=1.5
  • scipy >=1.13
  • seaborn >=0.13
  • statsmodels >=0.14
  • typer >=0.9