aq-qualhisto.1

.\" Authors: Andre Masella
.TH aq-qualhisto 1 "October 2011" "1.2" "USER COMMANDS"
.SH NAME 
aq-qualhisto \- Produce some quality statistics from FASTQ files
.SH SYNOPSIS
.B aq-qualhisto
[
.B \-j
] 
.B \-f 
.I file.fastq
.SH DESCRIPTION
This produces quality statistics from Illumina FASTQ input files. Standard output contains the length, average quality score, quality score standard deviation and quality-mask region length for each sequence and standard error contains, as a function of the number of uncalled bases in the sequence, the average quality score, quality score deviation and percentage of degenerate nucleotides.

This is mostly mean to be used internally by 
.BR aq-qualityanal (1).
.SH OPTIONS
.TP
\-f
The FASTQ file to be examined.
.TP
\-j
The input file is compressed with
.BR bzip (1).
.SH SEE ALSO
.BR aq-qualityanal (1),
.BR axiome (1).