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Bioinformatics Pipeline

Build and run end-to-end bioinformatics workflows as pipelines

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 DesignerBuild and run bioinformatics pipelines


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bioinfo.pipeline.PipelinePipeline object to build and run end-to-end bioinformatics analyses and workflows
bioinfo.pipeline.BlockBlock object for Bioinformatics pipeline
bioinfo.pipeline.blocks.BamSortBioinformatics pipeline block to sort BAM files
bioinfo.pipeline.blocks.Bowtie2Bioinformatics pipeline block to align sequencing reads to reference sequences
bioinfo.pipeline.blocks.Bowtie2BuildBioinformatics pipeline block to create Bowtie2 index from reference sequence
bioinfo.pipeline.blocks.BwaIndexBioinformatics pipeline block to create BWA indices from reference sequences
bioinfo.pipeline.blocks.BwaMEMBioinformatics pipeline block to map sequence reads to reference genome
bioinfo.pipeline.blocks.CuffCompareBioinformatics pipeline block to compare assembled transcripts
bioinfo.pipeline.blocks.CuffDiffBioinformatics pipeline block to identify significant changes in transcript expression
bioinfo.pipeline.blocks.CuffMergeBioinformatics pipeline block to merge transcript assemblies
bioinfo.pipeline.blocks.CufflinksBioinformatics pipeline block to assemble transcriptome from aligned reads
bioinfo.pipeline.blocks.CuffNormBioinformatics pipeline block to normalize transcript expression levels
bioinfo.pipeline.blocks.CuffQuantBioinformatics pipeline block to quantify gene and transcript expression profiles
bioinfo.pipeline.blocks.FeatureCountBioinformatics pipeline block to count reads mapped to genomic features
bioinfo.pipeline.blocks.FileChooserBioinformatics pipeline block to select files or URLs
bioinfo.pipeline.blocks.SamSortBioinformatics pipeline block to sort SAM files
bioinfo.pipeline.blocks.SeqFilterBioinformatics pipeline block to filter sequences
bioinfo.pipeline.blocks.SeqSplitBioinformatics pipeline block to split sequences into separate files
bioinfo.pipeline.blocks.SeqTrimBioinformatics pipeline block to trim sequences
bioinfo.pipeline.blocks.UserFunctionBioinformatics pipeline block to call custom function
bioinfo.pipeline.InputInput port object for bioinformatics pipeline block
bioinfo.pipeline.OutputOutput port object for bioinformatics pipeline block
bioinfo.pipeline.datatypes.FileFile object for bioinformatics pipeline
bioinfo.pipeline.datatypes.IncompleteIncomplete pipeline result object
bioinfo.pipeline.datatypes.UnsetUnset input port value
SeqFilterOptionsContain options to filter sequences
SeqSplitOptionsContain options to split sequences based on barcodes
SeqTrimOptionsContain options to trim sequences based on specified criterion
FeatureCountOptionsContain options to compute number of reads mapped to genomic features


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addBlockAdd blocks to pipeline
blockNameReturn the names of specified blocks in pipeline
cancelCancel blocks in pipeline that are running in parallel
compileVerify pipeline structure and check for warnings and errors
connectConnect two blocks in pipeline
copyCopy array of handle objects
deleteResultsDelete block results from pipeline
disconnectRemove connection between ports in a pipeline
fetchResultsWait for parallel-running block to finish and return its results
findBlockGet block objects from bioinformatics pipeline
inputNamesGet names of unconnected block inputs from pipeline
portMapShow connected ports between two blocks
processTableReturn information about all processes in pipeline
removeBlockRemove blocks from pipeline
renameBlockRename block in pipeline
resultsGet bioinformatics pipeline results
runRun pipeline
waitWait for running blocks to complete
compilePerform block-specific additional checks and validations
copyCopy array of handle objects
emptyInputsCreate input structure for use with run method
evalEvaluate block object
runRun block object
unwrapDisplay full file path and name