.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH FASTQ-STATS "1" "July 2015" "fastq-stats 1.1.2" "User Commands"
.SH NAME
fastq-stats \- ea-utils: produce lots of easily digested statistics
.SH SYNOPSIS
.B fastq-stats
[\fI\,options\/\fR] \fI\,<fastq-file>\/\fR
.SH DESCRIPTION
Version: 1.01 $Id: fastq\-stats.cpp 652 2013\-09\-17 17:40:32Z earonesty $
.PP
Produces lots of easily digested statistics for the files listed
.PP
Options
.PP
\fB\-c\fR     cyclemax: max cycles for which following quality stats are produced [35]
\fB\-w\fR INT window: max window size for generating duplicate read statistics [2000000]
\fB\-d\fR     debug: prints out debug statements
\fB\-D\fR     don't do duplicate read statistics
\fB\-s\fR INT number of top duplicate reads to display
\fB\-x\fR FIL output fastx statistics (requires an output filename)
\fB\-b\fR FIL output base breakdown by per phred quality at every cycle.
.IP
It sets cylemax to longest read length
.PP
\fB\-L\fR FIL Output length counts
.PP
The following data are printed to stdout:
.TP
reads
: #reads in the fastq file
.TP
len
: read length. mean and stdev are provided for variable read lengths
.TP
phred
: phred scale used
.TP
window\-size
: Number of reads used to generate duplicate read statistics
.TP
cycle\-max
: Number of bases to assess for duplicity
.TP
dups
: Number of reads that are duplicates
.TP
%dup
: Pct reads that are duplcate
.TP
unique\-dup seq
: Number sequences that are duplicated
.TP
min dup count
: Smallest duplicate tally for any duplicate sequence
.TP
dup seq <rank> <count> <sequence>
: Lists top 10 most frequent duplicate reads along with count mean and stdev
.TP
qual
: Base Quality min, max and mean
.TP
%A,%T,%C,%G
: base percentages
.TP
total bases
: total number of bases