# Adding Reference Aligner Indexes

Note that this task is for adding indexes for alignment to the whole genome. If you want to align to the transcriptome or another set of genomic features, see [*Adding Aligner Indexes Based on an Annotation Model*](https://help.partek.illumina.com/partek-flow/user-manual/settings/components/library-file-management/adding-aligner-indexes-based-on-an-annotation-model).

Click the **+ Add reference aligner indexes** button under the *Reference aligner indexes* section header on the [library file management page](https://help.partek.illumina.com/partek-flow/user-manual/settings/components/library-file-management/library-file-management-page). Choose the aligner index you wish to add from the drop-down list in the *Add aligner index* dialog (Figure 1). The following indexes can be added:

* Bowtie
* Bowtie 2
* HISAT 2
* TMAP
* BWA
* GSNAP
* GSNAP v8
* STAR
* STAR 2.5.3a
* STAR 2.7.3a
* STAR 2.7.8a
* Issac 2
* RSEM
* Salmon
* Cell Ranger ARC 2.0.0 reference
* Minimap2

![Figure 1. Add aligner index dialog.  For many model organisms, automatic downloads are available from the Partek repository](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c3578eb9703f601abb20b34d703ee7affdf10efa%2Fadd-aligner-dialog%20\(1\).png?alt=media)

If you are using an assembly supported by Partek (e.g. human), there are three radio button options: *Download index*; *Build index* or *Import index* (Figure 1). Certain aligner indexes may not be available for automatic download because the file sizes are too large to download efficiently.

If available, select **Download index** and click **Create** to get the chosen reference aligner index from the Partek repository.

Alternatively, select **Build index** and click **Create** to build the reference aligner index. To build an aligner index, a reference sequence file must already be associated with the assembly. Depending on the aligner, you may have to specify further parameters. Consult the user documentation for each aligner for guidance (usually available on-line).

Alternatively, select **Import index** and click **Create** to add an aligner index from another source. An aligner index can be added from the *Partek Flow Server* or a *URL* download link. The behavior of each option is similar to when importing a reference sequence (see [*Adding a Reference Sequence*](https://help.partek.illumina.com/partek-flow/user-manual/settings/components/library-file-management/adding-a-reference-sequence)). When browsing for files on the Partek Flow server, only the files with relevant file extensions will be visible. This will vary for each aligner.

For custom assemblies (e.g. for non-model organisms), only the *Build index* and *Import index* options are available (Figure 2).

![Figure 2. For custom assemblies, automatic downloads are not available so the aligner indexes has to be built or imported](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-7f2616d6800871024d25b28354e8bad91a90989d%2Fadd-aligner-dialog-non-model.png?alt=media)

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.