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gen: DNA Sequence Generator

Overview

The DNA Sequence Generator is a C program designed to create random DNA sequences in FASTA or FASTQ format focusing on some parameters focusing on their lengths. It generates multiple files containing sequences of varying lengths.

This tool is particularly useful for:

  • Testing tools to gather statistics from DNA sequences
  • Benchmarking bioinformatics pipelines

Features

  • Calculates and includes N50 statistics in the output filenames
  • Supports both FASTA and FASTQ output formats
  • Deterministic output based on a provided seed for reproducibility
  • Output filename format: N50_TOTSEQS_SUMLEN.{fasta|fastq} to make easy to test the N50 calculation

Compilation

To compile the program, use a C compiler such as GCC:

gcc -o dna_generator dna_generator.c -lm

Usage

./gen <min_seqs> <max_seqs> <min_len> <max_len> <tot_files> <format> <outdir>

Parameters

  • <min_seqs>: Minimum number of sequences per file
  • <max_seqs>: Maximum number of sequences per file
  • <min_len>: Minimum length of each sequence
  • <max_len>: Maximum length of each sequence
  • <tot_files>: Total number of files to generate
  • <format>: Output format (either "fasta" or "fastq")
  • <outdir>: Directory to store the output files
  • <seed>: Seed for the random number generator (for reproducibility)

Example

gen  10 100 1000 10000 5 fasta output_dir

This command will generate 5 FASTA files in the output_dir directory. Each file will contain between 10 and 100 sequences, with lengths ranging from 1000 to 10000 base pairs. The random number generator will be initialized with a static seed to ensure reproducibility.

Output

The program generates files with names in the format:

${N50}_${TOTSEQS}_${SUMLEN}.{fasta|fastq}

Where:

  • N50 is the N50 statistic of the sequences in the file
  • TOTSEQS is the total number of sequences in the file
  • SUMLEN is the sum of all sequence lengths in the file

FASTA Format

In FASTA format, each sequence is represented as:

>seq1
ATCGATCGATCG...
>seq2
GCTAGCTAGCTA...

FASTQ Format

In FASTQ format, each sequence is represented as:

@seq1
ATCGATCGATCG...
+
IIIIIIIIIIII...
@seq2
GCTAGCTAGCTA...
+
IIIIIIIIIIII...

Note: The quality scores in FASTQ format are dummy values (all 'I') for simplicity.

License

This program is provided under the MIT License. See the source code for full license text.

Author

Andrea Telatin, 2023 Quadram Institute Bioscience