calc_fastq-stats

calc_fastq-stats.pl is a script to calculate basic statistics for bases and reads in a FASTQ file.

• Synopsis
• Description
• Usage
• Options
  • Mandatory options
  • Optional options
• Output
• Run environment
• Dependencies
• Author - contact
• Citation, installation, and license
• Changelog

Synopsis

perl calc_fastq-stats.pl -i reads.fastq

or

gzip -dc reads.fastq.gz | perl calc_fastq-stats.pl -i -

Description

The script calculates some simple statistics, like individual and total base counts, GC content, and basic stats for the read lengths, and read/base qualities in a FASTQ file. The GC content calculation does not include 'N's. Stats are printed to STDOUT and optionally to an output file.

Because the quality of a read degrades over its length with all NGS machines, it is advisable to also plot the quality for each cycle as implemented in tools like FastQC or the fastx-toolkit.

If the sequence and the quality values are interrupted by line breaks (i.e. a read is not represented by four lines), please fix with Heng Li's seqtk:

seqtk seq -l 0 infile.fastq > outfile.fastq

An alternative tool, which is a lot faster, is fastq-stats from ea-utils.

Usage

zcat reads.fastq.gz | perl calc_fastq-stats.pl -i - -q 64 -c 175000000 -n 3000000

Options

Mandatory options

• -i, -input

Input FASTQ file or piped STDIN (-) from a gzipped file

• -q, -qual_offset

ASCII quality offset of the Phred (Sanger) quality values [default 33]

Optional options

• -h, -help:

Help (perldoc POD)

• -c, -coverage_limit

Number of bases to sample from the top of the file

• -n, -num_read

Number of reads to sample from the top of the file

• -o, -output

Print stats in addition to STDOUT to the specified output file

• -v, -version

Print version number to STDERR

Output

• STDOUT

Calculated stats are printed to STDOUT

• (outfile)

Optional outfile for stats

Run environment

The Perl script runs under Windows and UNIX flavors.

Dependencies

If the following modules are not installed get them from CPAN:

• Statistics::Descriptive

Perl module to calculate basic descriptive statistics

• Statistics::Descriptive::Discrete

Perl module to calculate descriptive statistics for discrete data sets

• Statistics::Descriptive::Weighted

Perl module to calculate descriptive statistics for weighted variates

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Citation, installation, and license

For citation, installation, and license information please see the repository main README.md.

Changelog

• v0.1 (28.10.2014)