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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 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.


Biopipeline DesignerBuild and run bioinformatics pipelines (Since R2023a)


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bioinfo.pipeline.PipelinePipeline object to build and run end-to-end bioinformatics analyses and workflows (Since R2023a)
bioinfo.pipeline.BlockBlock object for Bioinformatics pipeline (Since R2023a)
bioinfo.pipeline.block.Bowtie2Bioinformatics pipeline block to align sequencing reads to reference sequences (Since R2023a)
bioinfo.pipeline.block.Bowtie2BuildBioinformatics pipeline block to create Bowtie2 index from reference sequence (Since R2023a)
bioinfo.pipeline.block.BwaIndexBioinformatics pipeline block to create BWA indices from reference sequences (Since R2023a)
bioinfo.pipeline.block.BwaMEMBioinformatics pipeline block to map sequence reads to reference genome (Since R2023a)
bioinfo.pipeline.block.CuffCompareBioinformatics pipeline block to compare assembled transcripts (Since R2023a)
bioinfo.pipeline.block.CuffDiffBioinformatics pipeline block to identify significant changes in transcript expression (Since R2023a)
bioinfo.pipeline.block.CuffMergeBioinformatics pipeline block to merge transcript assemblies (Since R2023a)
bioinfo.pipeline.block.CufflinksBioinformatics pipeline block to assemble transcriptome from aligned reads (Since R2023a)
bioinfo.pipeline.block.CuffNormBioinformatics pipeline block to normalize transcript expression levels (Since R2023a)
bioinfo.pipeline.block.CuffQuantBioinformatics pipeline block to quantify gene and transcript expression profiles (Since R2023a)
bioinfo.pipeline.block.FeatureCountBioinformatics pipeline block to count reads mapped to genomic features (Since R2023a)
bioinfo.pipeline.block.GenomicsViewerOpen Genomics Viewer (Since R2024a)
bioinfo.pipeline.block.BLASTNCreate BLASTN query block (Since R2024a)
bioinfo.pipeline.block.BLASTPCreate BLASTP query block (Since R2024a)
bioinfo.pipeline.block.BLASTXCreate BLASTX query block (Since R2024a)
bioinfo.pipeline.block.TBLASTNCreate TBLASTN query block (Since R2024a)
bioinfo.pipeline.block.TBLASTXCreate TBLASTX query block (Since R2024a)
bioinfo.pipeline.block.MakeBlastDatabaseCreate local BLAST database (Since R2024a)
bioinfo.pipeline.block.FileChooserBioinformatics pipeline block to select files or URLs (Since R2023a)
bioinfo.pipeline.block.UserFunctionBioinformatics pipeline block to call custom function (Since R2023a)
bioinfo.pipeline.block.SRAFasterqDumpDownload NGS data from SRA (Since R2024a)
bioinfo.pipeline.block.SRASAMDumpDownload SAM files from SRA (Since R2024a)
bioinfo.pipeline.block.BamSortBioinformatics pipeline block to sort BAM files (Since R2023a)
bioinfo.pipeline.block.SamSortBioinformatics pipeline block to sort SAM files (Since R2023a)
bioinfo.pipeline.block.SeqFilterBioinformatics pipeline block to filter sequences (Since R2023a)
bioinfo.pipeline.block.SeqSplitBioinformatics pipeline block to split sequences into separate files (Since R2023a)
bioinfo.pipeline.block.SeqTrimBioinformatics pipeline block to trim sequences (Since R2023a)
bioinfo.pipeline.library.LibraryCollection of blocks to use in bioinformatics pipelines (Since R2023b)
bioinfo.pipeline.InputInput port object for bioinformatics pipeline block (Since R2023a)
bioinfo.pipeline.OutputOutput port object for bioinformatics pipeline block (Since R2023a)
bioinfo.pipeline.datatype.FileFile object for bioinformatics pipeline (Since R2023a)
bioinfo.pipeline.datatype.IncompleteIncomplete pipeline result object (Since R2023a)
bioinfo.pipeline.datatype.UnsetUnset input port value (Since R2023a)
SeqFilterOptionsContain options to filter sequences (Since R2023a)
SeqSplitOptionsContain options to split sequences based on barcodes (Since R2023a)
SeqTrimOptionsContain options to trim sequences based on specified criterion (Since R2023a)
FeatureCountOptionsContain options to compute number of reads mapped to genomic features (Since R2023a)


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addBlockAdd blocks to pipeline (Since R2023a)
blockNameReturn the names of specified blocks in pipeline (Since R2023a)
cancelCancel blocks in pipeline that are running in parallel (Since R2023a)
compileVerify pipeline structure and check for warnings and errors (Since R2023a)
connectConnect two blocks in pipeline (Since R2023a)
copyCopy array of handle objects
deleteResultsDelete block results from pipeline (Since R2023a)
disconnectRemove connection between ports in a pipeline (Since R2023a)
fetchResultsWait for parallel-running block to finish and return its results (Since R2023a)
findBlockGet block objects from bioinformatics pipeline (Since R2023a)
inputNamesGet names of unconnected block inputs from pipeline (Since R2023a)
portMapShow connected ports between two blocks (Since R2023a)
processTableReturn information about all processes in pipeline (Since R2023a)
removeBlockRemove blocks from pipeline (Since R2023a)
renameBlockRename block in pipeline (Since R2023a)
resultsGet bioinformatics pipeline results (Since R2023a)
runRun pipeline (Since R2023a)
waitWait for running blocks to complete (Since R2023a)
compilePerform block-specific additional checks and validations (Since R2023a)
copyCopy array of handle objects
emptyInputsCreate input structure for use with run method (Since R2023a)
evalEvaluate block object (Since R2023a)
runRun block object (Since R2023a)
unwrapDisplay full file path and name (Since R2023a)
addBlockAdd block to library (Since R2023b)
findBlockFind blocks from block library (Since R2023b)
removeBlockRemove blocks from block library (Since R2023b)
renameBlockRename block in block library (Since R2023a)
bioinfo.pipeline.library.addLibraryAdd block library (Since R2023b)
bioinfo.pipeline.library.getLibraryGet block libraries (Since R2023b)
bioinfo.pipeline.library.loadLibraryLoad block library from file (Since R2023b)
bioinfo.pipeline.library.removeLibraryRemove block library (Since R2023b)
bioinfo.pipeline.library.saveLibrarySave block library to MAT-file (Since R2023b)