ReadUnt_Sim

For assistance, contact Sam Holt at sam_holt30@hotmail.co.uk

Quick Start

Download run.py and library.py and run from the command line:

python3 run.py <input file> [OPTS]

Examples can be found in example.md.

Requirements

The following modules must be installed:

• numpy
• matplotlib

Read Until Simulator

This script is intended to simulate a nanopore sequencing experiment with and without read until applied, to offer an estimate of the benefit in a given circumstance. An input file must be provided, to describe the input DNA and its coverage goals. The hours values output by the script should not be taken as accurate estimates of the duration of a given experiment. This is because the script only simulates a single nanopore.

Speed

-s option allows setting of sequencing speed. This is the rate at which DNA is allowed through pores, in bases per second.

Mean Read Length

-c option is used in a gamma distribution function to generate reads but is not itself the mean read length. The script readgen.py can assist in determining an appropriate value for a desired mean read length.

Interval

-i is the time taken to acquire a new read after one finishes, in seconds.

Rejection Penalty

-r is the time penalty incurred in order to reject a read, in seconds.

Identification lag

-l is the amount of bases which must be sequenced in order for read until to be able to map it to the reference and make a decision on whether to reject.

Input Files

The input file must be a tab-separated value file in which each line describes something in the input library. These may be individual chromosomes, whole genomes, or anything else required. The columns are as follows:

Size in base pairs  |  Relative Copy Number   |   Desired Coverage    |    Name

Other Files In This Repository

There are other Python scripts in this repository besides run.py and library.py. These include:

• average.py
  • Accepts a list of .tsv files of same shape and size, and attempts to average corresponding values.
• npore.py
  • This was intended to be used in a more detailed simulation which would have included multiple nanopores. It is incomplete.
• readgen.py
  • Can be used to help determine what scale value should be used in the run.py -c option to give a desired mean read length
• replace.py
  • This was used in the results of some metagenomics experiments to replace genome percentage values with base percentage values. It is not written for generalised usage
• specimen_plot.ipynb
  • A Jupyter Notebook which was used as a base from which to create specific plots of results