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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 : #reads in the fastq file

len : read length. mean and stdev are provided for variable read lengths

phred : phred scale used

: Number of reads used to generate duplicate read statistics

: 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

: base percentages

total bases
: total number of bases

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