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+seq_format-converter
+====================
+
+A script to convert a sequence file to another format.
+
+## Synopsis
+
+    perl seq_format-converter.pl -i seq_file.gbk -f gbk -o embl
+
+## Description
+
+This script converts a (multi-)sequence file of a specific format to a differently formatted output file. The most common sequence formats are: **embl**, **fasta**, and **gbk** (genbank).
+
+Since sequence formats change from time to time, BioPerl is not always up to date. For all available BioPerl sequence formats see: http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats. **Warning**: The *bioperl-ext* package and the *io_lib* library from the **Staden** package (http://staden.sourceforge.net/) need to be installed in order to read the scf, abi, alf, pln, exp, ctf, ztr formats.
+
+## Usage
+
+    perl seq_format-converter.pl -i seq_file -f in_format -o out_format
+
+### UNIX loop to reformat all sequence files in the current working directory
+
+    for i in *.[embl|gbk]; do perl seq_format-converter.pl -i $i -f [embl|gbk] -o [embl|fasta|gbk]; done
+
+## Options for *seq_format-converter.pl*
+
+### Mandatory options
+
+* -i, -input
+
+Input sequence file
+
+* -f, -format
+
+Input sequence format (e.g. 'embl' or 'gbk)
+
+* -o, -out_format
+
+Output sequence format (e.g. 'embl', 'fasta' or 'gbk)
+
+### Optional options
+
+* -h, -help
+
+Print usage
+
+* -v, -version
+
+Print version number
+
+## Output
+
+* seq_file.[embl|fasta|gbk]
+
+Output sequence file in the specified format
+
+## Run environment
+
+The Perl script runs under Windows and UNIX flavors.
+
+## Dependencies (not in the core Perl modules)
+
+* BioPerl (tested with version 1.006901)
+
+## 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
+
+* v0.2 (03.02.2014)
+    - allow short 'gbk' format instead of 'genbank'
+    - also short 'gbk' file-extension for output file
+    - included 'use autodie'
+    - usage as HERE document
+    - options with Getopt::Long
+    - version switch
+* v0.1 (10.11.2011)