or use some freeware like gsplit. Be remember to give the lines in mutiples of 4 [4 lines per read].

install http://www.cygwin.org , and use split

If you're familiar with R, you can use the ShortRead library to break the file up into smaller files. It's only a few lines of code. The example below takes a fastq file, breaks it up into sets of 1 million reads, writing the results to incrementally named smaller files:

library(ShortRead)

# set the file (.gz files also work)
yourFile <- "foo.fastq"
fileBaseName <- sub(".fastq$","",yourFile)
# iterate over fastq file
f <- FastqStreamer(yourFile, 1000000)
file_index <- 0
while (length(fq <- yield(f))) {
  newName <- paste(fileBaseName, "_", file_index,".fastq", sep="")
  writeFastq(fq,file=newName)
  file_index <- file_index + 1
}
close(f)

You should be able to do this with Powershell, if you don't want to install Cygwin. Use a read count and a modulus operation on four lines, as Sukhdeep suggests.

Hi

i am very glad to use this short program. but I like to know how I will change the output file folder. For e.g. have the big FastqFile in folder E:/Sequencing/input/ERR127_1.fastq.gz now I want to make it small 1000000 reads/file and want to save it in folder E:/Sequencing/output how I will do that ? I did

# set the file (.gz files also work)
FastqFile <- "./Sequencing/ERR127306_1.fastq.gz"
fileBaseName <- sub(".fastq$","", FastqFile)
# iterate over fastq file
f <- FastqStreamer(FastqFile, 1000000)
file_index <- 0
while (length(fq <- yield(f))) {
  newName <- paste(Sequencing/output, "/", fileBaseName, "_", file_index,".fastq", sep="")
  writeFastq( fq, file=newName)
  file_index <- file_index + 1
}
close(f)

i am getting this error

Error in eval(expr, envir, enclos) : object 'Sequencing' not found
> close(f)

how to fix it? plz reply I need your help