Bioinformatics Pipeline

A bioinformatics pipeline is a set of connected algorithms (or blocks) that are executed in a predefined order to process and analyze next-generation sequencing (NGS) data locally or in cluster environments. Bioinformatics Toolbox™ provides an app and programmatic tools to build end-to-end bioinformatics pipelines to perform analyses on genomic data. You can build a pipeline interactively using a block diagram editor or programmatically using the MATLAB^® language.

The toolbox provides several built-in blocks that perform specific tasks, such as filtering genomic reads or mapping reads to a reference genome. In addition, you can also convert any custom function into a block that you can use in a pipeline. Using a combination of built-in blocks and custom blocks enables you to build various analysis workflows and pipelines. For instance, you can create a pipeline that can preprocess reads, map them to a reference genome, count reads that are mapped to genomic features, and perform a statistical analysis, such as a differential expression analysis or genome-wide analysis from RNA-Seq or ChIP-Seq data.