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README.md

Examples

Run E. coli Example

Commands

  1. Go to a directory to store fmlrc and clone this repository:
git clone https://github.com/holtjma/fmlrc.git
  1. Change into the fmlrc example directory:
cd fmlrc/example
  1. Run the examples script. This will automatically install ropebwt2 to a local path, download short- and long-read E. coli data, build the multi-string BWT using ropebwt2 and fmlrc-convert, and lastly run use fmlrc to correct the first 400 reads in the long-read data:
./run_example.sh

Outputs

  1. ./ecoli_comp_msbwt.npy - this contains the run-length encoded multi-string BWT using the same encoding as the msbwt python package. Note: if you wish to use this with msbwt, it will need to be placed in it's own directory and renamed to comp_msbwt.npy in that directory. For more information, please refer to the msbwt wiki pages.
  2. ./corrected_final.fa - this contains the first 400 long reads after correction using fmlrc.