get_all_combinations: Get all compatible combinations.

In comoto-pasteur-fr/DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

Get all compatible combinations.

Description

Finds the exhaustive set of compatible barcode combinations.

Usage

get_all_combinations(index_df, mplex_level, platform)

Arguments

index_df	A dataframe containing barcodes identifiers, corresponding DNA sequences along with GC content and presence of homopolymers.
mplex_level	The number at which the barcodes will be multiplexed. Illumina recommends to not multiplex more than 96 libraries.
platform	An integer representing the number of channels (1, 2, 4) of the desired Illumina platform: 1 for iSeq; 2 for NextSeq, NovaSeq, MiniSeq; 4 for HiSeq and MiSeq. 0 represents any other platform than Illumina.

Details

Be aware that the total number of combinations may become prohibitively large for large barcode sets and large multiplexing numbers.

Value

A matrix containing the identifiers of compatible barcode combinations.

See Also

get_random_combinations

Examples

get_all_combinations(DNABarcodeCompatibility::IlluminaIndexes, 2, 4)

comoto-pasteur-fr/DNABarcodeCompatibility documentation built on Sept. 17, 2024, 3:28 p.m.