https://github.com/danderson123/masters_project

https://github.com/danderson123/masters_project

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/danderson123/masters_project
• Owner: Danderson123
• License: cc0-1.0
• Created: 2020-05-14T11:04:11.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-10-26T13:06:07.000Z (about 4 years ago)
• Last Synced: 2023-08-15T00:29:54.002Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 7.32 MB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Overview

This repository houses the scripts for my MSc in Epidemiology project "A pan-genomic functional annotation framework integrating genomic epidemiology and functional genomics". 

# Motivation 

There are currently no tools capable of functionally annotating bacterial genomes with the consistency and efficiency needed for high throughput genomic epidemiology. 

# Methods 

* retrieve_sequences.py: Retrieve genomic sequences in FASTA format and functional annotations in GFF format using Biopython Entrez, then quality control and re-format for direct input into Panaroo. This script also outputs an "all_annotations.csv" file that is later the source of functional annotations. 

* retrieve_samples.py: Used for high throughput sequence retrieval as Biopython Entrez has a tendency to crash in these situtations. 

* Panaroo: Used to construct the "reference" pan-genome that clusters input features (https://github.com/gtonkinhill/panaroo).

* update_descriptions.py: Transfer clustered gene names in the Panaroo output to "all_annotations.csv"

* update_annotations.py: Update functional annotation files for isolates already in the graph

* integrate.py: Integrate the functional annotations for a single isolate into a Panaroo graph to incorporate newly characterised genomic information. 

* gen_index.py: Construct a COBS index from a Panaroo reference output (https://github.com/bingmann/cobs). 

* annotate.py: Functionally annotate a genome in fasta format using a Panaroo-updated "all_annotations.csv" and COBS-constructed index. Features are annotated by consensus between Panaroo and COBS. If they disagree, the names identified by both tools are included.