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To add a new assembly, click on Settings -> Library files. From the Assembly drop-down list, select Add assembly and specify a the species. If the species name is not in the list, choose Other, Other and type in the species name with the assembly version (you may have multiple assembly versions can exist for one species, e.g. hg19 and hg38 for Homo Sapiens). You need to add the reference file which is a .fasta file containing sequence information. Once the reference file is added, you can build any aligner index to perform the alignment task. 

The Annotation model is a file containing feature location; this . This file can be used to quantify to an annotation model in RNA-Seq analysis, or to annotate variant or peaks in a DNA-Seq or ATAC-Seq/ChIP-Seq data analysis pipeline. The file format should be .gtf/.gff/.bed.

We recommend looking for the species files of the species on the Ensembl website. There is no need to unzip or save these files to your local machine, instead right click and copy the link address of the specific file (not a link to a folder). For more details, here is the documentation chapter: Library File Management - Partek® Documentation. 

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