This C++ program extracts and counts specific sequences from fastq files.
On a mac terminal - the program can be compiled using: % g++ *.cpp -o readcounter
Then run using: % ./readcounter
After selecting a csv file containing all contig sequences to be searched (single contig per line) and the fastq file to be analysed ... two output files will be generated:
- Output.csv
- which contains the sequence string and frequency of identical occurences in the fastq file
- Output.fastq
- which contains the sequences and accompanying information for the reads which have an identical matching sequence string to the input file