/ONSRGA

ONTSRGA algorithm is designed to simulate the generation of sequencing reads from a given reference genome, mimicking the error characteristics typical of Oxford Nanopore sequencing technology.

Primary LanguagePython

ONSRGA: Oxford Nanopore Sequencing Read Generator Algorithm

This algorithm is designed to simulate the generation of sequencing reads from a given reference genome, mimicking the error rate characteristics typical of Oxford Nanopore sequencing technology.

Algorithm Description:

  • Input/Output: algorithm takes a string of nucleic acid (i.e. reference genome) and returns a list of sequence reads according to the hypergeometric probability distribution (i.e. sampling without replacement).
  • Functionality: algorithm breaks the string (input) into smaller fragments (output) that are within the desired input size (min, max). It will then add errors (substitutions or deletions) to each read to simulate Oxford Nanopore sequencing error rates per read.

Screen Shot 2020-12-15 at 7 57 17 AM

Read generation process: Screenshot 2022-11-15 at 10 39 17 PM