BARCOSEL

BARCOSEL selects optimal subsets of DNA barcode sequences for multiplexed high-throughput sequencing to minimize sample misidentification by enforcing sequence distinctness and balanced nucleotide composition.

Key Features:

• Optimal Barcode Selection: Selects an optimal barcode set from a user-provided pool of candidate sequences while enforcing sequence-space distinctness and per-position nucleotide balance.
• Compatibility Checking: Assesses whether predefined barcode sets can be combined into a single sequencing pool without compromising accuracy.
• Barcode Augmentation: Expands existing barcode sets by selecting additional barcodes from candidate sequences to reach a desired set size.
• Optimization Engine: Defines a cost function and constraints from the desired number of barcodes and candidate sequences and solves the combinatorial problem using integer programming with a core algorithm implemented in C.

Scientific Applications:

• Multiplexed high-throughput sequencing: Enables reliable pooling of multiple samples by reducing misassignment due to sequencing errors and imbalanced nucleotide usage.
• Metagenomics: Supports multiplexed metagenomic studies by providing barcode sets that maintain sample discrimination across complex communities.
• Transcriptomics: Facilitates multiplexed transcriptomic experiments by optimizing barcode design to preserve accurate sample demultiplexing.

Methodology:

Formulates barcode selection as a minimization problem with an explicit cost function and constraints generated from user-specified candidate sequences and desired barcode count, solved by integer programming; the core algorithm is implemented in C.