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+order_fastx
+===========
+
+`order_fastx.pl` is a script to order sequences in FASTA or FASTQ files.
+
+* [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 order_fastx.pl -i infile.fasta -l order_id_list.txt > ordered.fasta
+
+## Description
+
+Order sequence entries in FASTA or FASTQ sequence files according to
+an ID list with a given order. Beware, the IDs in the order list
+have to be **identical** to the entire IDs in the sequence file.
+
+However, the ">" or "@" ID identifiers of FASTA or FASTQ files,
+respectively, can be omitted in the ID list.
+
+The file type is detected automatically. But, you can set the file
+type manually with option **-f**. FASTQ format assumes **four** lines
+per read, if this is not the case run the FASTQ file through
+[`fastx_fix.pl`](/fastx_fix) or use Heng Li's [`seqtk
+seq`](https://github.com/lh3/seqtk):
+
+    seqtk seq -l 0 infile.fq > outfile.fq
+
+The script can also be used to pull a subset of sequences in the ID
+list from the sequence file. Probably best to set option flag **-s**
+in this case, see [Optional options](#optional-options) below. But, rather use
+[`filter_fastx.pl`](/filter_fastx).
+
+## Usage
+
+    perl order_fastx.pl -i infile.fq -l order_id_list.txt -s -f fastq > ordered.fq
+
+    perl order_fastx.pl -i infile.fasta -l order_id_list.txt -e > ordered.fasta
+
+## Options
+
+### Mandatory options
+
+- -i, -input
+
+    Input FASTA or FASTQ file
+
+- -l, -list
+
+    List with sequence IDs in specified order
+
+### Optional options
+
+- -h, -help
+
+    Help (perldoc POD)
+
+- -f, -file_type
+
+    Set the file type manually [fasta|fastq]
+
+- -e, -error_files
+
+    Write missing IDs in the seq file or the order ID list without an equivalent in the other to error files instead of *STDERR* (see [Output](#output) below)
+
+- -s, -skip_errors
+
+    Skip missing ID error statements, excludes option **-e**
+
+- -v, -version
+
+    Print version number to *STDERR*
+
+## Output
+
+- *STDOUT*
+
+    The newly ordered sequences are printed to *STDOUT*. Redirect or pipe into another tool as needed.
+
+- (order_ids_missing.txt)
+
+    If IDs in the order list are missing in the sequence file with option **-e**
+
+- (seq_ids_missing.txt)
+
+    If IDs in the sequence file are missing in the order ID list with option **-e**
+
+## 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 (20.11.2014)