What Software Exists For Barcode Sorting Of Multiplexed Sequences?

Question

[Andrewjgrimm]

What software exists for sorting multiplexed sequences by their barcode from the same next-generation sequencing run?

(Note: this is talking about DNA barcoding as in distinguishing sequences by an artificial sequence added to an existing sequence, not as in identifying the species of a biological sample based on DNA analysis, the latter described by Wikipedia here)

[mikhail.shugay]

Try this one https://100bp.wordpress.com/2013/05/08/barcode-splitting-of-ngs-data/. Allows flexible match (several mismatches and redundant DNA characters), two-sided barcoding (to get rid of contamination) and extraction of molecular counter regions (for error correction).

Answer 1

[Michael]

The FASTX tools contain the FASTX barcode splitter. Can also be used with Galaxy.

[Johnmu]

But this does not support pair-end sequences.

Answer 2

[Andrewjgrimm]

BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. - C and C++ based.

split_libraries.py – Split libraries according to barcodes specified in mapping file - Python library (I think - could be part of a larger python package).

Answer 3

[User 59]

NextGene from BioGene/Softgenetics http://www.biogene.com/datasheets/softgenetics_nextgene_software.cfm also has barcode sorting if you were looking for a commercial package.

Answer 4

[Malcolm.Cook]

depending on your barcoding scheme?

If you have paired-end Illumina fastq formatted results with barcode on both ends, I've got a short perl script employing perl Bio::SeqIO. Not too fast, but it ensures that same barcode is present on both ends. (Also, the CASAVA suite from Illumina version 1.7 is supposed to provide some barcode de-multiplexing capability, but I've not tried it yet).