Hnoss

Introduction

Hnoss is an extension of the Freyja¹ SARS-CoV-2 strain deconvolution package² to allow for easier manipulation and more flexibility.

Table of Contents

• Introduction
• Dependencies
• Installation
• Input
• Output
• Workflow
• References

Dependencies

See environment.yml and requirements.txt for package dependancies.

Installation

Install with pip:

$ pip install git+https://github.com/provlab-bioinfo/hnoss

Access in python:

>>> import hnoss

Input

This tool runs after Freyja via a flexible import functions. For strain deconvolution, it allows any combination of output files from freyja demix and freyja aggregate. Please refer to the Freyja documentation.

Output

Typical Hnoss structure:

SampleInfo			SummarizedLineages				RawLineages
file	resid	coverage	Alpha	Beta	XBB* (XBB.X)	...	A.1	BA.2.1	XBB.1.11	...
230101_1_S1_L001.variants.tsv	8.28	98.475	0.121	0.312	0.426	...	NA	0.061	0.678	...
230101_2_S2_L001.variants.tsv	9.42	99.234	0.015	0.168	0.767	...	0.002	0.007	0.362	...
...	...	...	...	...	...	...	...	...	...	...

References

1. Karthikeyan, Smruthi, et al. "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission (preprint)." (2021).

2. Andersen-Lab Andersen-Lab/Freyja: Depth-weighted De-Mixing https://github.com/andersen-lab/Freyja (accessed Oct 4, 2023).