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+calc_fastq-stats
+================
+
+`calc_fastq-stats.pl` is a script to calculate basic statistics for bases and reads in a FASTQ file.
+
+* [Synopsis](#synopsis)
+* [Description](#description)
+* [Usage](#usage)
+* [Options](#options)
+  * [Mandatory options](#mandatory-options)
+  * [Optional options](#optional-options)
+* [Output](#output)
+* [Run environment](#run-environment)
+* [Dependencies](#dependencies)
+* [Author - contact](#author---contact)
+* [Citation, installation, and license](#citation-installation-and-license)
+* [Changelog](#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](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+or the [fastx-toolkit](http://hannonlab.cshl.edu/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](https://github.com/lh3/seqtk):
+
+    seqtk seq -l 0 infile.fastq > outfile.fastq
+
+An alternative tool, which is a lot faster, is **fastq-stats** from
+[ea-utils](https://code.google.com/p/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](http://www.cpan.org/):
+
+- `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](https://github.com/aleimba/bac-genomics-scripts#citation), [installation](https://github.com/aleimba/bac-genomics-scripts#installation-recommendations), and [license](https://github.com/aleimba/bac-genomics-scripts#license) information please see the repository main [*README.md*](https://github.com/aleimba/bac-genomics-scripts/blob/master/README.md).
+
+## Changelog
+
+- v0.1 (28.10.2014)