edittag 1.1

Design and check sets of edit metric sequence tags

  Add it to your Download Basket!

 Add it to your Watch List!

0/5

Rate it!
send us
an update
LICENSE TYPE:
BSD License 
USER RATING:
UNRATED
  0.0/5
DEVELOPED BY:
Brant Faircloth
HOMEPAGE:
baddna.github.com
CATEGORY:
ROOT \ Science and Engineering \ Bioinformatics
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

requirements

#metric sequence #sequence tags #check sets #metric #sequence #tags #sets

Add your review!

SUBMIT