DNABarcodes-package: Create and analyse DNA barcode sets that are capable of error...

In DNABarcodes: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

Description

The package offers a function to create DNA barcode sets capable of correcting substitution errors or insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.

Details

Package:	DNABarcodes
Type:	Package
Version:	0.1
Date:	2014-07-23
License:	GPL-2

The function create.dnabarcodes creates a set of barcodes of equal length that satisfies some wished criteria regarding error correction.

After sequencing the DNA/RNA material, the researcher will have a set of reads that start with a (possibly mutated) barcode. For Illumina HiSeq, this is the index read. For PacBio, this is the read itself (with some other complications). The function demultiplex can then be used to assign reads to their original reference barcodes. demultiplex will correct mutations in a best-effort way.

Existing sets of barcodes (e.g. supplied by a manufacturer) can be analysed with functions analyse.barcodes and barcode.set.distances.

The advantage of this package over using already available barcode sets in the scientific community is the ability to flexibly generate new barcode sets of different properties. For example, create.dnabarcodes can use a pre-existing barcode library as a candidate set for a better barcode set. In another example, a higher distance (e.g., dist = 4) can be used. Such a parameter setting would possibly increase the error detection property of the code as well as the average barcode distance, increasing the probability of guessing a barcode during demultiplexing.

Author(s)

Tilo Buschmann ([e-mail])

References

Buschmann, T. and Bystrykh, L. V. (2013) Levenshtein error-correcting barcodes for multiplexed DNA sequencing. BMC bioinformatics, 14(1), 272. Available from http://www.biomedcentral.com/1471-2105/14/272.

Levenshtein, V. I. (1966). Binary codes capable of correcting deletions, insertions and reversals. In Soviet physics doklady (Vol. 10, p. 707).

Hamming, R. W. (1950). Error detecting and error correcting codes. Bell System technical journal, 29(2), 147-160.

Conway, J. and Sloane, N. (1986) Lexicographic codes: error-correcting codes from game theory. Information Theory, IEEE Transactions on, 32(3), 337-348.

Pattabiraman, B., Patwary, M. M. A., Gebremedhin, A. H., Liao, W. K. and Choudhary, A. (2013) Fast algorithms for the maximum clique problem on massive sparse graphs. In Algorithms and Models for the Web Graph (pp. 156-169). Springer International Publishing.

Ashlock, D., Guo, L. and Qiu, F. (2002) Greedy closure evolutionary algorithms. In Computational Intelligence, Proceedings of the World on Congress on (Vol. 2, pp. 1296-1301). IEEE.

Brouwer, A. E., Shearer, L. B. and Sloane, N. I. A. (1990) A new table of constant weight codes. In IEEE Trans Inform Theory.

Examples

# Create Sequence Levenshtein Barcodes with the default heuristic
dnabarcodes1 <- create.dnabarcodes(5, metric="seqlev")

# Create Sequence Levenshtein Barcodes with a better, but slower heuristic
dnabarcodes2 <- create.dnabarcodes(5, metric="seqlev", heuristic="ashlock")

Example output

Loading required package: Matrix
Loading required package: parallel
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
1) Creating pool ...  of size 592
2) Conway closing...  done 
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
1) Creating pool ...  of size 592
2) Initiating Chromosomes done 
3) Running Greedy Evolutionary done 

DNABarcodes documentation built on Nov. 8, 2020, 5 p.m.