README.md

rebar

rebar is a REcombination BARcode detector!

Why rebar?

1. rebar detects and visualizes genomic recombination.

   It follows the PHA4GE Guidance for Detecting and Characterizing SARS-CoV-2 Recombinants which outlines three steps:

   1. Assess the genomic evidence for recombination.
   2. Identify the breakpoint coordinates and parental regions.
   3. Classify sequences as designated or novel recombinant lineages.

2. rebar peforms generalized clade assignment.

   While specifically designed for recombinants, rebar works on non-recombinants tool! It will report a sequence's closest known match in the dataset, as well any mutation conflicts that were observed. The linelist and visual outputs can be used to detect novel variants, such as the SARS-CoV-2 pango-designation process.

3. rebar is for exploring hypotheses.

   The recombination search can be customized to test your hypotheses about which parents and genomic regions are recombining. If that sounds overwhelming, you can always just use the pre-configured datasets (ex. SARS-CoV-2) that are validated against known recombinants.

Install

rebar is a standalone binary file that you can simply download and run:

wget -O rebar https://github.com/phac-nml/rebar/releases/latest/download/rebar-x86_64-unknown-linux-musl
./rebar --help

• Please see the install docs for Windows, macOS, Docker, Singularity, and Conda.
• Please see the compile docs for those interested in source compilation.

Usage

Custom Dataset

A small, test dataset (toy1) serves as a template for creating custom datasets, and for easer visualization of the method and output.

rebar dataset download --name toy1 --tag custom --output-dir dataset/toy1
rebar run --dataset-dir dataset/toy1 --populations "*" --mask 0,0 --min-length 3 --output-dir output/toy1
rebar plot  --run-dir output/toy1 --annotations dataset/toy1/annotations.tsv

SARS-CoV-2

Download a SARS-CoV-2 dataset, version-controlled to the date 2023-11-30 (try any date!).

rebar dataset download --name sars-cov-2 --tag 2023-11-30 --output-dir dataset/sars-cov-2/2023-11-30
rebar run --dataset-dir dataset/sars-cov-2/2023-11-30  --populations "AY.4.2*,BA.5.2,XBC.1.6*,XBB.1.5.1,XBL" --output-dir output/sars-cov-2
rebar plot --run-dir output/sars-cov-2 --annotations dataset/sars-cov-2/2023-11-30/annotations.tsv

Other

Please see the examples docs for more tutorials including:

• Using your own alignment of genomes as input.
• Testing specific parent combinations.
• Performing a 'knockout' experiment.
• Validating all populations in a dataset.

Please see the dataset and run docs for more methodology.

Output

Linelist

A linelist summary of results (ex. output/toy1/linelist.tsv).

strain	validate	validate_details	population	recombinant	parents	breakpoints	edge_case	unique_key	regions	genome_length	dataset_name	dataset_tag	cli_version
population_A	pass		A				false			20	toy1	custom	0.2.0
population_B	pass		B				false			20	toy1	custom	0.2.0
population_C	pass		C				false			20	toy1	custom	0.2.0
population_D	pass		D	D	A,B	12-12	false	D_A_B_12-12	1-11|A,12-20|B	20	toy1	custom	0.2.0
population_E	pass		E	E	C,D	4-4	false	E_C_D_4-4	1-3|C,4-20|D	20	toy1	custom	0.2.0

Plots

A visualization of substitutions, parental origins, and breakpoints (ex. output/toy1/plots/).

Barcodes

The discriminating sites with mutations between samples and their parents (ex. output/toy1/barcodes/).

coord	origin	Reference	A	B	population_D
1	A	A	C	T	C
2	A	A	C	T	C
3	A	A	C	T	C
4	A	A	C	T	C
5	A	A	C	T	C
...	...	...	...	...	...

Credits

rebar is built and maintained by Katherine Eaton at the National Microbiology Laboratory (NML) of the Public Health Agency of Canada (PHAC).

This project follows the all-contributors specification (emoji key). Contributions of any kind welcome!

Katherine Eaton 💻 📖 🎨 🤔 🚇 🚧

Special thanks go to the following people, who are instrumental to the design and data sources in rebar:

• Lena Schimmel (@lenaschimmel) for the original concept of a barcode-scanning recombinant detector with sc2rf.
• Cornelius Roemer (@corneliusroemer) for the designated lineages, consensus sequences, and Nextclade barcodes.
• Josh Levy (@joshuailevy) and the Andersen Lab for the UShER barcodes from Freyja.
• Richard Neher (@rneher) and the Neher Lab for python package structure, specifically treetime.

Lena Schimmel 🤔

Cornelius Roemer 🔣 🔣 🔣

Josh Levy 🔣

Richard Neher 🤔

Thanks go to the following people, who participated in the development of rebar and ncov-recombinant:

Yatish Turakhia 🔣 🤔	Angie Hinrichs 🔣 🤔	Benjamin Delisle 🐛 ⚠️	Vani Priyadarsini Ikkurthi 🐛 ⚠️	Mark Horsman 🤔 🎨	Dan Fornika 🤔 ⚠️	Tara Newman 🤔 ⚠️
Adrian Zetner 🔣 🤔	Connor Chato 🔣 🤔	Matthew Wells 📦	Andrea Tyler 🔣