NucBalancer: Streamlining Barcode Sequence Selection for Optimal Sample Pooling for Sequencing

Abstract

Recent advancements in next-generation sequencing (NGS) technologies have brought to the forefront the necessity for versatile, cost-effective tools capable of adapting to a rapidly evolving landscape. The emergence of numerous new sequencing platforms, each with unique sample preparation and sequencing requirements, underscores the importance of efficient barcode balancing for successful pooling and accurate demultiplexing of samples. Recently launched new sequencing systems claim better affordability comparable to more established platforms further exemplifies these challenges, especially when libraries originally prepared for one platform need conversion to another. In response to this dynamic environment, we introduce NucBalancer, a Shiny app developed for the optimal selection of barcode sequences. While initially tailored to meet the nucleotide, composition challenges specific to G400 and T7 series sequencers, NucBalancers utility significantly broadens to accommodate the varied demands of these new sequencing technologies. Its application is particularly crucial in single-cell genomics, enabling the adaptation of libraries, such as those prepared for 10x technology, to various sequencers including G400 and T7 series sequencers. By facilitating the efficient balancing of nucleotide composition and the accommodation of differing sample concentrations, NucBalancer plays a pivotal role in reducing biases in nucleotide composition. This enhances the fidelity and reliability of NGS data across multiple platforms. As the NGS field continues to expand with the introduction of new sequencing technologies, the adaptability and wide-ranging applicability of NucBalancer render it an invaluable asset in genomic research. This tool addresses the current sequencing challenges ensuring that researchers can effectively balance barcodes for sample pooling regardless of the sequencing platform used. Availability and implementationNucBalancer is implemented in R and is available at https://github.com/ersgupta/NucBalancer. Additionally, a shiny interface is made available at https://ersgupta.shinyapps.io/NucBalancer/.