simON-reads v2.0.1

Added the handling of haplotype phasing information, now the command should look like this:

simON_reads.py -i ref.fa -n 3000 --enable_homopolymer_error --enable_sequencing_error -snp "locus1:222:C>G:0,locus1:279:C>T:1,locus2:23:G>A:1,locus2:534:C>G:0" > individual1.fastq

simON-reads v2.0.0

Major adjustments in the SNPs generating function: now it is able to generate diploid-like distribution of SNPs correctly.

simON-reads v1.1.0

Added the following options, to enable a wider control of the output:

-ehp, --enable_homopolymer_error  : This will set a 30% chance of getting an extra nucleotide around homopolymeric regions
-ese, --enable_sequencing_error   : This will set a 5% chance of getting a random single nucleotide variant or insertion, while it retains also a 5% 
chance of skipping a base (single deletion)

The command line will thus look like this:

simON_reads.py -i reference.fasa -n 1000 -snp "SAMPLE:POS:REF>ALT,SAMPLE:POS:REF>ALT" --enable_sequencing_error --enable_homopolymer_error

simON-reads v1.0.0

simON-reads ("Simulate Oxford Nanopore Reads") is a simple yet powerful tool to generate fastq files containing MiniON-like long reads: this python script generates artificial DNA sequencing reads with specified variations and errors for given reference sequences. It utilizes the BioPython library for handling DNA sequences and provides options to introduce single nucleotide polymorphisms (SNPs) and sequencing errors.
simON-reads, thus, represent a flexible and customizable tool for generating artificial DNA sequencing data, making it valuable for testing and validating bioinformatics softwares and pipelines. The introduced variations and errors simulate real-world scenarios, allowing for thorough testing of downstream analysis pipelines.