bioinfo.pipeline.block.Bowtie2
Bioinformatics pipeline block to align sequencing reads to reference sequences
Since R2023a
Description
A Bowtie2
block enables you to map sequencing reads to reference
sequences.
The block requires the Bowtie 2 Support Package for Bioinformatics Toolbox™. If this support package is not installed, then a download link is provided. For details, see Bioinformatics Toolbox Software Support Packages.
Creation
Syntax
Description
creates a
b
= bioinfo.pipeline.block.Bowtie2Bowtie2
block.
also specifies additional alignment b
= bioinfo.pipeline.block.Bowtie2(options
)options
.
also specifies the output file name.b
= bioinfo.pipeline.block.Bowtie2(OutFilename=fileName
)
specifies additional options as the property names and values of a b
= bioinfo.pipeline.block.Bowtie2(Name=Value
)Bowtie2AlignOptions
object. This object is set as the value of the
Options
property of the block. For example, bt2Block =
bioinfo.pipeline.block.Bowtie2(Trim5=10)
sets the Trim5
property of the object to trim 10 residues from the 5' end.
Input Arguments
Properties
Object Functions
compile | Perform block-specific additional checks and validations |
copy | Copy array of handle objects |
emptyInputs | Create input structure for use with run method |
eval | Evaluate block object |
run | Run block object |
Examples
References
[1] Langmead, Ben, and Steven L Salzberg. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9, no. 4 (April 2012): 357–59. https://doi.org/10.1038/nmeth.1923.
Version History
Introduced in R2023a