damaged-reads-simulator 0.1.1

A simulator for damaged DNA reads with base quality recalibration

Damaged reads_simulator

Simulates NGS sequenced reads

Installation

python3 -m venv readsim_env
source readsim_env/bin/activate

pip install damaged-reads-simulator

for prototyping with marimo:

pip install marimo matplotlib seaborn

Usage

simulate-reads <parameters.info>

as a default, if no path was provided, it will use ./parameters.info

where parameters.info file should be as follows.

# SYNTAX IS IMPORTANT
# LInes starting with # are comments
# name of the parameter: value
# : not = | where True/False first letter is uppercase.
random seed: 402

# GENOME SIMULATION PARAMETERS
reference file path: None
generate reference: True
GC percentage: 40
length of contigs: 1000000,10000,50000,200000 

# READS SIMULATION PARAMETERS
number of reads: 100000
read_length: 76
insert length: 100
insert length variations: 35
type of library: FFPE

# METHYLATION PARAMETERS
methylation library: False
percent methylation: 96

# PREFIX TO BE USED IN LOG AND OUTPUT FILES
prefix: ffpe_nometh

The above should be modified to your needs.

Important considerations

Some systematic artifacts have a very low frequency and simulating few reads might not be enough to include even traces of it. In such case, use a higher number of reads (try one or more ordens of magnitude).