seqtk

#to subsample 100K reads from a large fastq file
seqtk sample -s 100 read1.fq 100000 > sub1.fq

#to subsample the same 100K reads from both files from a paired end sequence
seqtk sample -s 10 read1.fq 1000 > sub1.fastq
seqtk sample -s 10 read2.fq 1000 > sub2.fastq

Usage:   seqtk <command> <arguments>
Version: 1.2-r101-dirty

Command: seq       common transformation of FASTA/Q
         comp      get the nucleotide composition of FASTA/Q
         sample    subsample sequences
         subseq    extract subsequences from FASTA/Q
         fqchk     fastq QC (base/quality summary)
         mergepe   interleave two PE FASTA/Q files
         trimfq    trim FASTQ using the Phred algorithm

         hety      regional heterozygosity
         gc        identify high- or low-GC regions
         mutfa     point mutate FASTA at specified positions
         mergefa   merge two FASTA/Q files
         famask    apply a X-coded FASTA to a source FASTA
         dropse    drop unpaired from interleaved PE FASTA/Q
         rename    rename sequence names
         randbase  choose a random base from hets
         cutN      cut sequence at long N
         listhet   extract the position of each het