Bioinformatics Toolbox™ provides support packages for various next-generation sequencing workflows and analyses. To make a support package available in your MATLAB® command line, you must first install it.
Follow these steps to install a support package.
In the Environment section of the MATLAB toolstrip, select Add-Ons > Get Add-Ons.
In the Add-On Explorer, search for the support package that you want to install by entering its name.
Install the support package.
For details about installing add-ons, see Get and Manage Add-Ons. For other information, see Add-Ons.
The following table lists all the Bioinformatics Toolbox support packages that are available for download as Add-Ons.
Support Package Name | Version† | Corresponding MATLAB functions | Supported OS |
|---|---|---|---|
Bioinformatics Toolbox Interface for Bowtie Aligner [1] |
| Mac and UNIX® | |
Cufflinks Support Package for the Bioinformatics Toolbox [2] |
|
| Mac and UNIX |
| Mac and UNIX |
†Version of the original (third-party) software
[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.
[2] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.
[3] Mortazavi, Ali, Brian A Williams, Kenneth McCue, Lorian Schaeffer, and Barbara Wold. “Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq.” Nature Methods 5, no. 7 (July 2008): 621–28. https://doi.org/10.1038/nmeth.1226.
[4] Li, Heng, and Richard Durbin. “Fast and Accurate Long-Read Alignment with Burrows–Wheeler Transform.” Bioinformatics 26, no. 5 (March 1, 2010): 589–95. https://doi.org/10.1093/bioinformatics/btp698.
[5] Li, Heng, and Richard Durbin. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics 25, no. 14 (July 15, 2009): 1754–60. https://doi.org/10.1093/bioinformatics/btp324.