edittag

edittag is an application collection for designing sets of edit metric sequence tags, checking sequence tags for conformation to the edit metric, and integrating sequence tags to platform-specific sequencing adapters and PCR primers. edittag differs from other approaches:

 * edittag generates arbitrary lengths of edit-metric sequence tags in reasonable time frames using multiprocessing
 * edittag produces edit metric sequence tag sets conform to the edit distance selected
 * edittag used primer3 to integrate sequence tags to PCR primers

We provide several large sets of edit metric sequence tags designed using edittag in the following formats:

 * text - this file is in an appropriate format for check_levenshtien_distance.py
 * csv
 * sqlite database

Citation

Faircloth BC, Glenn TC. Large sets of edit-metric sequence identification
tags to facilitate large-scale multiplexing of reads from massively
parallel sequencing. doi_

Installation:

easy_install

easy_install edittag

tar.gz

wget package.tar.gz
tar -xzf package.tar.gz
python setup.py install

repository

git clone git://github.com/baddna/edittag.git edittag

optional package (py-levenshtein)

wget http://pylevenshtein.googlecode.com/files/python-Levenshtein-0.10.1.tar.bz2
tar -xzvf python-Levenshtein-0.10.1.tar.bz2
python setup.py install

optional package (primer3)

If you wish to design primers incorporating edit metric sequence tags, you need to first install a modified version of primer3:

git clone git://github.com/baddna/mod-primer3.git
cd mod-primer3/src
make
make install

Ensure that you move the binaries from mod-primer3 to a location in your path (move at least primer3-long and primer3_config into the same directory in your path). You can then run

Requirements:

• Python
• NumPy
• Levenshtein
• mod-primer3