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Design and check sets of edit metric sequence tags.

Project description

Copyright (c) 2009-2012 Brant C. Faircloth. All rights reserved.


edittag is a software 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:


You can find documentation here:


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



  • tar.gz
  • repository



easy_install edittag


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


git clone git:// edittag

optional package (py-levenshtein)

tar -xzvf python-Levenshtein-0.10.1.tar.bz2
python 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://
cd mod-primer3/src

Ensure that you move the binaries from mod-primer3 to a location in your path (move at least primer3-long and primer3_config into identical directories in your path).


# Testing requires numpy and nose
import edittag

Using edittag

# generate some tags
% --tag-length=6 --edit-distance=3 \
    --no-polybase --gc --comp --min-and-greater --output tmp/tags.txt

# validate the 6 nucleotide, edit distance 3 tag set
    --section='6nt ed3'

# add those tags to a primer set
    --input tmp/tags.txt --section='6nt ed3'
    --sort=pair_hairpin_either,pair_penalty,cycles \
    --remove-common --keep-database \
    --output tmp/trnH_tagged_with_10_nt_ed_5_tags.csv

Project details

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Files for edittag, version 1.1
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