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