NAME

       fastq-stats - ea-utils: produce lots of easily digested statistics

SYNOPSIS

       fastq-stats [options] <fastq-file>

DESCRIPTION

       Version: 1.01 $Id: fastq-stats.cpp 652 2013-09-17 17:40:32Z earonesty $

       Produces lots of easily digested statistics for the files listed

       Options

       -c      cyclemax:  max  cycles  for which following quality stats are produced [35] -w INT
       window: max window size for generating duplicate read statistics [2000000]  -d      debug:
       prints out debug statements -D     don't do duplicate read statistics -s INT number of top
       duplicate reads to display -x FIL output fastx statistics (requires an output filename) -b
       FIL output base breakdown by per phred quality at every cycle.

              It sets cylemax to longest read length

       -L FIL Output length counts

       The following data are printed to stdout:

       reads  : #reads in the fastq file

       len    : read length. mean and stdev are provided for variable read lengths

       phred  : phred scale used

       window-size
              : Number of reads used to generate duplicate read statistics

       cycle-max
              : Number of bases to assess for duplicity

       dups   : Number of reads that are duplicates

       %dup   : Pct reads that are duplcate

       unique-dup seq
              : Number sequences that are duplicated

       min dup count
              : Smallest duplicate tally for any duplicate sequence

       dup seq <rank> <count> <sequence>
              : Lists top 10 most frequent duplicate reads along with count mean and stdev

       qual   : Base Quality min, max and mean

       %A,%T,%C,%G
              : base percentages

       total bases
              : total number of bases