Introduction to MetaScope

Aubrey Odom1*, Rahul Varki2** and W. Evan Johnson3***

1Program in Bioinformatics, Boston University, Boston, MA
2Research Assistant in Johnson Lab, Boston University School of Medicine, Boston, MA
3The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA

*aodom@bu.edu
**rvarki@bu.edu
***wej@bu.edu

Package

MetaScope 1.5.4

Contents

1 Important Note

Although it is not a requirement, MetaScope will fun faster and more efficiently for larger samples if the samtools package is present on your device. You can download it at https://github.com/samtools/samtools.

2 Introduction

MetaScope is a complete metagenomics profiling package that can accurately identify the composition of microbes within a sample at a strain-level resolution. MetaScope can be considered as an updated and expanded R translation of PathoScope 2.0, a Python-based metagenomic profiling package created by the Johnson lab. A few improvements made in MetaScope include using the BAM file format instead of the SAM file format for significantly less disk space usage, removing all dependencies to NCBI’s now defunct GI sequence annotations, and properly filtering reads that align to filter reference genomes. Functions to analyze host microbiome data are also planned to be added in future updates to the package.

2.1 MetaScope Workflows

The major workflow of MetaScope is delineated below. It is composed of core modules that are formed by groups of functions.