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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

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