NGS-paired-end-reads-fastq-generator

A python program used to generate a perfect NGS paired-end reads fastq file. It's created for simulation purpose. I used it to evaluate the performance of alignments, calling accuracy, etc.
Since it aims to create a "perfect" data, the phred quality score for each base is setted to "I". Reads are assumed to be uniformly distributed with a N(0,1) shift and probability of reverse complement is set to 0.5.

Requirement

pyhon3

pysam (pip install pysam)

Arguments

Fasta file at first place

-t1 Specified your target reference name. (must be identical with the name in fasta file)")

-t2 (potional) Specified another target reference name if you want to generate heterozigous data

-o Output file name without extention.

-r The average length of reads. (Default: 150)

-f The average length of DNA fragments. (Default: 450)

-d The average alignment depth. (Default: 30)

usage

Example for homozygous

python fastq_generator.py file.fasta -t1 HLA:HLA02169 -o output -r 150 -f 450 -d 30

It generates two fq files (output1.fq and output2.fq) for first read and second read.

Example for heterozygous

python fastq_generator.py file.fasta -t1 HLA:HLA02169 -t1 HLA:HLA02169 -t2 HLA:HLA15760 -o output_name -r 150 -f 450 -d 30

It generates two fq files (output1.fq and output2.fq) for first read and second read.

output

Output format

@simulate_targetname_1_read0/1
GATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCC...
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...