C script for logical subsampling of FASTQ reads

Features

Maintains Read Pairs: Always keeps or discards both R1 & R2 reads together to maintain pairing.

Configurable Subsampling: You can specify any subsampling fraction from 1% to 100%.

Random Seed Control: Allows setting a specific random seed for reproducible results.

Efficient Processing: Reads and writes FASTQ records in blocks of 4 lines.

Error Handling: Checks for file opening errors & unpaired reads at the end of files.

Verbose Output: Optionally reports statistics about the subsampling process.

1. C Script for Subsampling Paired-End FASTQ Reads

Compilation:

You'll need to link with zlib:

gcc -o subsample_paired_fastq subsample_paired_fastq.c -lz

Usage:

./subsample_paired_fastq -a input_R1.fastq.gz -b input_R2.fastq.gz -x output_R1.fastq -y output_R2.fastq -f 10 -z

2. C Script for Subsampling Single-End FASTQ Reads

Compilation:

You'll need to link with zlib:

gcc -o subsample_single_end_fastq.c -o subsample_single_end_fastq -lz

Usage:

# Subsample 20% with gzip-compressed output and verbose logs

./subsample_single_end_fastq -i input.fastq -o subsampled.fastq.gz -f 20 -z -v

3. This version:

Handles your gzipped input files

Gives you a clear error if the files are wrongly paired

Allows compressed output with -z

Provides more detailed information about any issues