> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/instruments.md).

# Instruments

DNAstack simplifies genomic data analysis by eliminating the need for expensive local infrastructure or specialized technical expertise. With Instruments, you can seamlessly connect your raw sequencing data to [Workbench](https://github.com/DNAstack/dnastack-product-docs/blob/main/docs/workbench/instruments/broken-reference/README.md), choose your [Engine](/products/workbench/engines.md), and launch a [workflow](/products/workbench/workflows.md)—all with ease.

## Overview

Instruments bridges the gap between primary sequencing data and advanced analysis workflows, and simplifying the process of connecting sequencing data to your Workbench workflow.

## Working with Instruments

DNAstack’s Instrument tool allows you to directly connect data from physical sequencing platforms to Workbench. Instruments represent physical sequencing platforms, such as PacBio, that upload sequencing run outputs to a cloud storage location.

### The Analysis Pipeline

**Primary Analysis**: Raw sequencing data from instruments into readable outputs.

**Secondary Analysis**: Applies quality control, alignment and variant calling to process sequencing data.

**Tertiary Analysis**: Interprets secondary processed data to uncover insights, validate findings, and drive scientific discovery.

## Terminology

* **Storage:** Operations pertaining to interacting with cloud storage from Workbench.
* **Storage Account**: The entity that is created when a user saves credentials using the storage command.
* **Platform**: A specific sequencing platform (e.g. PacBio, Illumina, Oxford Nanopore, etc.) that has uploaded the outputs of a sequencing run to a cloud storage location. Each platform has specific file naming and directory naming conventions for output data and various supporting files that are generated. If the user changes the names of files or the directory structure from what the sequencing platform generated, this will lead to undefined behavior.
* **Instrument:** An entity corresponding to a physical sequencing instrument.
* **Sample:** A biological sample (e.g. <mark style="color:green;">`hg013.m89015_220827.bam`</mark>). Samples are unique within a namespace.
* **File:** A file (e.g. FASTQ, BAM, VCF, etc.) belonging to a biological sample. Each file is associated with a sequencing platform and the specific instrument that generated it.


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