edittag 1.1

Design and check sets of edit metric sequence tags
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

last updated on:
July 14th, 2012, 18:24 GMT
price:
FREE!
homepage:
baddna.github.com
license type:
BSD License 
developed by:
Brant Faircloth
category:
ROOT \ Science and Engineering \ Bioinformatics
edittag
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