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bioinformatics pipeline -凯发k8网页登录

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.

apps

build and run bioinformatics pipelines

objects

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 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

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
run pipeline
wait for running blocks to complete
perform block-specific additional checks and validations
copy array of handle objects
create input structure for use with run method
evaluate block object
run block object
display full file path and name

topics


  • create a simple pipeline to plot the quality of sequence reads using the biopipeline designer app.


  • create a bioinformatics pipeline to count rna-seq reads that are mapped to genomic features.


  • use splitdimension to distribute input data across multiple runs of a block in a bioinformatics pipeline.


  • a bioinformatics pipeline automatically determines which blocks to rerun during iterative pipeline runs.


  • use the splitdimension property to distribute input data on individual blocks and perform independent executions of blocks.


  • download and install bioinformatics support packages for ngs workflows.

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