fplaza / fastq-sample

fastq-sample

fastq-sample performs simple random sampling of reads from FASTQ files.

Sampling modes

3 modes are available:

• random sampling of a target number of reads
• random sampling of a target number of bases
• random sampling of a target proportion of reads

Usage

• -f [ --fastq-files ] arg input FASTQ files (use /dev/fd/0 for stdin)
• -o [ --output-file ] arg output FASTQ file (use /dev/fd/1 for stdout)
• -r [ --target-num-reads ] arg number of reads to sample
• -b [ --target-num-bases ] arg number of bases to sample
• -p [ --target-proportion ] arg proportion of total reads to sample

Compilation requirements

• A C++ compiler (tested with gcc 4.4)
• Boost C++ Libraries