BridgeRNA2024

This code repository accompanies the paper "Bridge RNAs direct programmable recombination of target and donor DNA" by Durrant & Perry et al, 2024.

It includes snakemake pipelines and code for various key analyses described in the paper.

Contents

There are 5 separate pipelines in this code repository. Pipelines are meant to be run through the brna2024 command. Each pipeline includes a *.Snakefile and *.config.yml file. There is also a *.py file that contains the python functions for the pipeline. The *.py file is imported by the *.Snakefile and is used to implement the snakemake rules. There are also accompanying *.R files that contain R scripts that implement some of the rules.

rnaseq

• This pipeline was used to process the small RNA-seq data from WT donor plasmids of the IS621 and related orthologs and aligns them to the donor plasmids to detect the expression of the bridge RNAs.
• Related files
  • rnaseq.py
  • snakemake/rnaseq.Snakefile
  • snakemake/rnaseq.config.yml

structure

• This pipeline was used to detect the secondary structure of bridge RNAs in the flanks of the bridge recombinase CDS by the alignment of many homologous sequences.
• Related files
  • structure.py
  • snakemake/structure.Snakefile
  • snakemake/structure.config.yml

targetscreen

• This pipeline was used to process the amplicon sequencing data from the target screen experiments.
• Related files
  • targetscreen.py
  • snakemake/targetscreen.Snakefile
  • snakemake/targetscreen.config.yml

donorscreen

• This pipeline was used to process the amplicon sequencing data from the donor screen experiments.
• Related files
  • donorscreen.py
  • snakemake/donorscreen.Snakefile
  • snakemake/donorscreen.config.yml

nanoporepipeline

• This pipeline was used to process the nanopore sequencing data from the genomic insertion experiments.
• Related files
  • nanoporepipeline.py
  • snakemake/nanoporepipeline.Snakefile
  • snakemake/nanoporepipeline.config.yml

Note

This repository is for reference only. It is not guaranteed to work on your system, and will likely require modifications to run properly. The Dockerfile can be useful for installing some of the dependencies. Once working, it is intended to be used as follows:

brna2024 <pipeline name> --threads <number of threads> <workdir>

or if you want to run the pipeline through docker:

source setup.sh;
brna2024_docker_run <pipeline name> <number of threads> <workdir>

Citation

Please cite our paper if you use any aspect of this code repository in your work.