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+rename_fasta_id
+===============
+
+`rename_fasta_id.pl` is a script to rename fasta IDs according to regular expressions.
+
+* [Synopsis](#synopsis)
+* [Description](#description)
+* [Usage](#usage)
+* [Options](#options)
+  * [Mandatory options](#mandatory-options)
+  * [Optional options](#optional-options)
+* [Output](#output)
+* [Run environment](#run-environment)
+* [Author - contact](#author---contact)
+* [Citation, installation, and license](#citation-installation-and-license)
+* [Changelog](#changelog)
+
+## Synopsis
+
+    perl rename_fasta_id.pl -i file.fasta -p "NODE_.+$" -r "K-12_" -n -a c > out.fasta
+
+**or**
+
+    zcat file.fasta.gz | perl rename_fasta_id.pl -i - -p "coli" -r "" -o > out.fasta
+
+## Description
+
+This script uses the built-in Perl substitution operator `s///` to
+replace strings in FASTA IDs. To do this, a **pattern** and a
+**replacement** have to be provided (Perl regular expression syntax
+can be used). The leading '>' character for the FASTA ID will be
+removed before the substitution and added again afterwards. FASTA
+IDs will be searched for matches with the **pattern**, and if found
+the **pattern** will be replaced by the **replacement**.
+
+**IMPORTANT**: Enclose the **pattern** and the **replacement** in
+quotation marks (' or ") if they contain characters that would be
+interpreted by the shell (e.g. pipes '|', brackets etc.).
+
+For substitutions without any appendices in a UNIX OS you can of
+course just use the great
+[`sed`](https://www.gnu.org/software/sed/manual/sed.html) (see
+`man sed`), e.g.:
+
+    sed 's/^>pattern/>replacement/' file.fasta
+
+## Usage
+
+    perl rename_fasta_id.pl -i file.fasta -p "T" -r "a" -c -g -o
+
+## Options
+
+### Mandatory options
+
+- -i, -input
+
+Input FASTA file or piped STDIN (-) from a gzipped file
+
+- -p, -pattern
+
+Pattern to be replaced in FASTA ID
+
+- -r, -replacement
+
+Replacement to replace the pattern with. To entirely remove the pattern use '' or "" as input for **-r**.
+
+### Optional options
+
+- -h, -help
+
+Help (perldoc POD)
+
+- -c, -case-insensitive
+
+Match pattern case-insensitive
+
+- -g, -global
+
+Replace pattern globally in the string
+
+- -n, -numerate
+
+Append a numeration/the count of the pattern hits to the replacement. This is e.g. useful to number contigs consecutively in a draft genome.
+
+- -a, -append
+
+Append a string after the numeration, e.g. 'c' for chromosome
+
+- -o, -output
+
+Verbose output of the substitutions that were carried out, printed to *STDERR*
+
+- -v, -version
+
+Print version number to *STDERR*
+
+## Output
+
+- *STDOUT*
+
+The FASTA file with substituted ID lines is printed to *STDOUT*. Redirect or pipe into another tool as needed.
+
+## Run environment
+
+The Perl script runs under Windows and UNIX flavors.
+
+## 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 (09.11.2014)