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To add a new assembly, click on Settings -> Library files. From the Assembly drop-down list, select Add assembly. Specify a species, if you can't find the species name in the list, choose Other, type in species name and assembly version (you might have multiple assembly versions on one species, e.g. hg19 and hg38 assembly version on Homo Sapiens. You need to add reference file which is a .fasta file containing sequence information. Once the reference file is addadded, you can build any aligner index to perform the alignment task. 

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

We recommend look looking for the 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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