Resources for Developing MetaScope

A curated list of literature, tutorials, and technical documentation to support the development and improvement of the MetaScope metagenomic profiling pipeline.

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📄 PathoScope Literature

• Comprehensive identification of pathogens in clinical samples by unbiased metagenomic sequencing

  This foundational paper introduces the original PathoScope framework for accurate pathogen identification using metagenomic sequencing data.

• PathoScope: Metagenomic strain identification using a likelihood-based scoring method

  Describes the underlying statistical model that enables strain-level classification from sequencing reads.

• PathoScope 2.0: A framework for strain identification in environmental or clinical samples

  Details improvements in accuracy and speed in PathoScope 2.0, supporting complex microbial profiling tasks.

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📘 PathoScope 2.0 Tutorial

• PathoScope 2.0 Extended Tutorial PDF

  A step-by-step guide explaining installation, configuration, and use of PathoScope 2.0 on real data.

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🫁 Case Study: Asthma and the Microbiome

• The airway microbiome in asthma: a case-control study

  Demonstrates an application of metagenomic profiling (including PathoScope) in the analysis of airway microbiota and its link to asthma.

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🔧 Rsubread

• Rsubread User Guide (PDF)

  The official vignette for using Rsubread, a fast alignment and feature counting package commonly used with metagenomic pipelines.

• Rsubread in Practice: Publication Summary

  A peer-reviewed article showcasing the performance and use cases of Rsubread.

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🧬 Biostrings and DNAStringSet

• Intro to Biostrings Objects (Kasper Hansen)

  An accessible guide to using DNAStringSet and related objects for string manipulation in genomics.

• Biostrings Lab Tutorial (Stanford)

  A practical lab for learning the basics of Biostrings operations in R.

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🗃 Working with SAM/BAM Files

• Rsamtools Overview

  Documentation for the Rsamtools package, which enables manipulation and querying of .sam and .bam files from R.

• SAM/BAM File Format Specification (HTS-specs)

  Technical reference for the SAM/BAM format, with a detailed explanation of file structure and headers (see page 10).

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🧭 Reference Genomes

• Overview of Reference Genomes (ScienceDirect)

  A high-level overview of what reference genomes are and their importance in sequence alignment and classification.

• PathoMap (PathoScope GitHub Wiki)

  Official documentation for PathoMap, a key reference database component of the PathoScope framework.