Create fasta and fastq files for practicing with alignment tools. These files are generated randomly and can be a conveniant alternative to real data when practicing with alignment tools or comparing performance of various algorithms. I use these programs to help create educational content.
1) simply clone this repo to your computer git clone <link to this repo>
2) compile the programs with your favorite c++ compiler.
eg. g++ create_fasta.cpp -o create_fasta and g++ create_fastq.cpp -o create_fastq
3) run the code and use the option -h for instructions. eg. ./create_fasta -h
create a fasta file called random_reads.fasta with 25 randomly generated sequences all between the length 250-500bp
./create_fasta -n 25 --min 250 --max 500 --out random_reads.fasta
create a fastq file that simulates 100 reads from 'human_genome.fasta'. each read is 200bp, phred quality is between ':' and 'A', where 1 in 50 reads are misreads.
./create_fastq -n 100 --min ':' --max 'A' -l 200 --brp .02 -i human_genome.fasta