floria - metagenomic read-based strain phasing

floria is a software package for strain-level phasing of metagenomic sequencing samples.

Given a BAM and a VCF file, floria clusters reads into strain-level clusters. Floria can:

• Works with short or noisy long reads (preferably long)

• Phase metagenomic reads or single genome reads

• Multithreaded, takes minutes per contig/genome

• Minimal parameter tuning and automatic determination of strain number

• Give informative visualizations and summary statistics

To get started, check out the table of contents below.

Note

This project is under active development.

Contents

• Introduction
• Quick start
• Tutorials
• Usage: input and output information
• Utility scripts and visualization
• How-to-guides