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

FASTQ-STATS(1) User Commands FASTQ-STATS(1)

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
July 2015 fastq-stats 1.1.2