DOKK / manpages / debian 10 / ea-utils / fastq-stats.1.en

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

fastq-stats [options] <fastq-file>

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


-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 in the fastq file
: read length. mean and stdev are provided for variable read lengths
: phred scale used
: Number of reads used to generate duplicate read statistics
: Number of bases to assess for duplicity
: Number of reads that are duplicates
: Pct reads that are duplcate
: Number sequences that are duplicated
: Smallest duplicate tally for any duplicate sequence
: Lists top 10 most frequent duplicate reads along with count mean and stdev
: Base Quality min, max and mean
: base percentages
: total number of bases
July 2015 fastq-stats 1.1.2