Need and Role of Scala Implementations in Bioinformatics

Next Generation Sequencing has resulted in the generation of large number of omics data at a faster speed that was not possible before. This data is only useful if it can be stored and analyzed at the same speed. Big Data platforms and tools like Apache Hadoop and Spark has solved this problem. However, most of the algorithms used in bioinformatics for Pairwise alignment, Multiple Alignment and Motif finding are not implemented for Hadoop or Spark. Scala is a powerful language supported by Spark. It provides, constructs like traits, closures, functions, pattern matching and extractors that make it suitable for Bioinformatics applications. This article explores the Bioinformatics areas where Scala can be used efficiently for data analysis. It also highlights the need for Scala implementation of algorithms used in Bioinformatics. Keywords—Scala; Big Data; Hadoop; Spark; Next Generation Sequencing; Genomics; RNA; DNA; Bioinformatics