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TagGD

Software for creating synthetic DNA barcodes ("tags"), and for demultiplexing these, i.e. tracing them back, from actual sequenced DNA reads.

Applications

TagGD contains two applications:

  1. Multiplexer: Creates a set of synthetic DNA barcodes of arbitrary length, along with information on the minimum Hamming edit distance between two barcodes. Barcodes can be created so as to avoid known sequences that could cause downstream interference, such as genomic content.
  2. Demultiplexer: Takes as input a set of known barcodes (that may or may not stem from 1 above), and relates reads containing sequenced barcodes back to the true barcodes. Information on edit distance, ambiguity, etc. are reported.

Benefits

The benefits of TagGD compared to some other demultiplexing utilities are that:

  • TagGD allows for scenarios where the number of barcodes is substantial (i.e. in the order of thousands or hundreds of thousands).
  • TagGD allows not only for substitutions in the the read sequence, but also insertions and deletions.

Reference

TagGD has been peer-reviewed and published here.

Manual

See the multiplexer manual here.

See the demultiplexer manual here.

Installation

The multiplexer is written in C++. See INSTALL and README in the corresponding folder for more information. NOTE: An older, more specialized version of the demultiplexer named "findIndexes" is also included.

The most up-to-date demultiplexer is written in Python and Cython. See INSTALL and README in the corresponding folder for more information.

Contact

The original TagGD was written by Paul Igor Costea and Pelin Sahlén (pelin.sahlen@scilifelab.se). Additions and rewrites have been made by Joel Sjöstrand (joel.sjostrand@sclifelab.se) and José Fernandez Navarro (jose.fernandez.navarro@scilifelab.se).

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