https://github.com/murrellgroup/chmmera.jl

https://github.com/murrellgroup/chmmera.jl

Last synced: 5 months ago
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• Host: GitHub
• URL: https://github.com/murrellgroup/chmmera.jl
• Owner: MurrellGroup
• License: mit
• Created: 2022-08-20T20:42:41.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2025-02-17T09:01:39.000Z (over 1 year ago)
• Last Synced: 2025-03-12T12:07:50.628Z (about 1 year ago)
• Language: Julia
• Homepage:
• Size: 418 KB
• Stars: 3
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# CHMMera.jl

[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://murrellgroup.github.io/CHMMera.jl/)

[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://opensource.org/license/MIT)

[![Coverage](https://codecov.io/gh/MurrellGroup/CHMMera.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/CHMMera.jl)

CHMMera.jl is a method for reference-based detection of chimeric DNA sequences.

Chimera detection is performed using a Hidden Markov Model (HMM) that models sequences as being generated from a single reference with mutations or from multiple references with mutations. We implemented two approaches to determine mutation rates:

- Discretizing mutation rates by creating a state for each mutation rate + template combination, called the Discretized Bayesian (DB) approach.

- Estimating a continuous per-reference mutation rate using the Baum-Welch (BW) algorithm.

## Example usage

```

julia> using CHMMera

julia> refs = ["ACGTACGTACGT", "ACCACCACCAAT"]

julia> queries = ["ACGTACACCAAT", "ACCACCACCAGT"]

julia> get_chimera_probabilities(queries, refs)

2-element Vector{Float64}:

 0.9956728308121604

 0.05863188730424695

julia> get_recombination_events(queries, refs; detailed = false)

2-element Vector{RecombinationEvents}:

 (recombinations = RecombinationEvent[(position = 7, left = 1, right = 2, left_state = 1, right_state = 2)], startingpoint = 1)

 (recombinations = RecombinationEvent[], startingpoint = 2)

julia> get_recombination_events(queries, refs; detailed = true)

2-element Vector{DetailedRecombinationEvents}:

 (recombinations = RecombinationEvent[(position = 7, left = 1, right = 2, left_state = 1, right_state = 2)], startingpoint = 1, pathevaluation = 0.995612088796054, logsiteprobabilities = [-0.007751384549707252, -0.006081763823303499, -0.00439756634058619, -0.00464963436088528, -0.01670468631375581, -0.7003603824992484, -4.360877076008885, -0.0003315532714940339, -1.1770957131840287e-5, -4.643262233303136e-6, -4.698595592046717e-5, -0.0017033680895343628])

 (recombinations = RecombinationEvent[], startingpoint = 2, pathevaluation = -Inf, logsiteprobabilities = Float64[])

```