This is the command fastq-stats that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use fastq-stats online using onworks.net services
