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 your analysis 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.
|Biopipeline Designer||Build and run bioinformatics pipelines|
|Pipeline object to build and run end-to-end bioinformatics analyses and workflows|
|Block object for Bioinformatics pipeline|
|Bioinformatics pipeline block to sort BAM files|
|Bioinformatics pipeline block to align sequencing reads to reference sequences|
|Bioinformatics pipeline block to create Bowtie2 index from reference sequence|
|Bioinformatics pipeline block to create BWA indices from reference sequences|
|Bioinformatics pipeline block to map sequence reads to reference genome|
|Bioinformatics pipeline block to compare assembled transcripts|
|Bioinformatics pipeline block to identify significant changes in transcript expression|
|Bioinformatics pipeline block to merge transcript assemblies|
|Bioinformatics pipeline block to assemble transcriptome from aligned reads|
|Bioinformatics pipeline block to normalize transcript expression levels|
|Bioinformatics pipeline block to quantify gene and transcript expression profiles|
|Bioinformatics pipeline block to count reads mapped to genomic features|
|Bioinformatics pipeline block to select files or URLs|
|Bioinformatics pipeline block to sort SAM files|
|Bioinformatics pipeline block to filter sequences|
|Bioinformatics pipeline block to split sequences into separate files|
|Bioinformatics pipeline block to trim sequences|
|Bioinformatics pipeline block to call custom function|
Input and Output Ports
|Input port object for bioinformatics pipeline block|
|Output port object for bioinformatics pipeline block|
|File object for bioinformatics pipeline|
|Incomplete pipeline result object|
|Unset input port value|
|Contain options to filter sequences|
|Contain options to split sequences based on barcodes|
|Contain options to trim sequences based on specified criterion|
|Contain options to compute number of reads mapped to genomic features|
Pipeline Object Functions
|Add blocks to pipeline|
|Return the names of specified blocks in pipeline|
|Cancel blocks in pipeline that are running in parallel|
|Verify pipeline structure and check for warnings and errors|
|Connect two blocks in pipeline|
|Copy array of handle objects|
|Delete block results from pipeline|
|Remove connection between ports in a pipeline|
|Wait for parallel-running block to finish and return its results|
|Get block objects from bioinformatics pipeline|
|Get names of unconnected block inputs from pipeline|
|Show connected ports between two blocks|
|Return information about all processes in pipeline|
|Remove blocks from pipeline|
|Rename block in pipeline|
|Get bioinformatics pipeline results|
|Wait for running blocks to complete|
- Create Simple Pipeline to Plot Sequence Quality Data Using Biopipeline Designer
Create a simple pipeline to plot the quality of sequence reads using the Biopipeline Designer app.
- Count RNA-Seq Reads Using Biopipeline Designer
Create a bioinformatics pipeline to count RNA-Seq reads that are mapped to genomic features.
- Split Input SAM files and Assemble Transcriptomes Using Bioinformatics Pipeline
SplitDimensionto distribute input data across multiple runs of a block in a bioinformatics pipeline.
- Bioinformatics Pipeline Run Mode
A bioinformatics pipeline automatically determines which blocks to rerun during iterative pipeline runs.
- Bioinformatics Pipeline SplitDimension
SplitDimensionproperty to distribute input data on individual blocks and perform independent executions of blocks.
- Bioinformatics Toolbox Software Support Packages
Download and install Bioinformatics support packages for NGS workflows.