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