--- title: NGS Automation --- [Skip to content](https://insights.opentrons.com/ngs-automation#main-content) [![Opentrons Logo and Droplet Mark](https://insights.opentrons.com/hs-fs/hubfs/LOGO.png?width=97&height=352&name=LOGO.png "Opentrons Logo and Droplet Mark")](https://opentrons.com/) # Automating NGS Every lab has its own resources and goals. When evaluating automation, you need to think through the transition in the context of your lab and your samples. In this eBook, we discuss: - Trends and current challenges in sequencing workflows - How automation can help you overcome NGS library prep bottlenecks - Benefits of automation – getting better results while saving time and money ### Automating NGS Library Prep - [Why automate NGS?](https://insights.opentrons.com/ngs-automation#hs_cos_wrapper_widget_1657655080875) - [NGS on the OT-2](https://insights.opentrons.com/ngs-automation#hs_cos_wrapper_widget_1657728881939) - [Reasearch spotlights](https://insights.opentrons.com/ngs-automation#hs_cos_wrapper_widget_1657744119811) - [Resources](https://insights.opentrons.com/ngs-automation#hs_cos_wrapper_widget_1657744139236) Find out if automating NGS is right for you. [DOWNLOAD EBOOK](https://insights.opentrons.com/lp/automating-ngs-library-prep?hsLang=en) INTRODUCTION ## Why automate NGS? NGS is a powerful tool, but many parts of the NGS workflow are complex, require a lot of repetitive pipetting and are prone to errors. Labs are increasingly turning to automation to help with their NGS workflows. Automating your NGS workflow can increase efficiency, reduce errors and save hands-on time. ## Automating library prep, normalization and pooling saves total workflow time and hands-on time NGS workflow from nucleic acid extraction through to sequencing prep, with two different example NGS library prep workflows shown --- ![](https://insights.opentrons.com/hubfs/NGS_Workflow_Chart.jpeg) --- ![image006 - Edited](https://insights.opentrons.com/hs-fs/hubfs/image006%20-%20Edited.png?width=1550&height=872&name=image006%20-%20Edited.png)   **NEW APPLICATION DATA!** ## Novel hyb capture targeted sequencing sample prep on OT-2 Are you looking to improve your hybridization-based targeted sequencing workflows? As an industry first, [Avida Biomed](https://avidabio.com/) has automated their novel Point-n-Seq® chemistry on OT-2, offering a 6-hour workflow, with just 10-15 mins hands-on time, without compromising NGS performance. [GET APP NOTE](https://insights.opentrons.com/hubfs/Applications/NGS/Automating%20Avidas%20Point-n-Seq%20Hyb%20TS%20Sample%20Prep%20App%20Note.pdf?hsLang=en) **WORKSTATION** ## Automate your NGS workflow on the OT-2 The OT-2 can automate your library prep and pre-sequencing workflows using any leading reagent or magnetic bead-based system on the market. Explore our popular NGS workstation, which includes all the hardware modules and consumables you need to start automating NGS immediately. [Shop NGS](https://opentrons.com/workstations/expanded-ngs-workstation/) ![NGS_Workstation 1](https://insights.opentrons.com/hs-fs/hubfs/NGS_Workstation%201.png?width=483&name=NGS_Workstation%201.png)   ### Library prep on the OT-2 [Watch the webinar ›](https://insights.opentrons.com/lp/webinar-live-fully-automated-ngs-library-prep-0?hsLang=en) [Download the application note ›](https://insights.opentrons.com/hubfs/Applications/NGS/Automating%20DNA%20Library%20Prep%20Illumina%20KAPA%20NEBNext%20App%20Note.pdf) ### Quantification, normalization and pooling on the OT-2 [Watch the webinar ›](https://insights.opentrons.com/lp/webinar-ngs-quantification-on-the-ot-2?hsLang=en) [Download the application note ›](https://insights.opentrons.com/hubfs/Applications/NGS/Automating%20DNA%20Library%20Quantification%20Normalization%20Pooling%20App%20Note.pdf?hsLang=en) > "We automated much of the \[OCTOPUS plasmid sequencing\] protocol using the open-source Opentrons OT-2 liquid handling system and reduced the necessary hands-on time by more than 70%." Bryan Jiang Research Associate, [Octant](https://www.octant.bio/) ## Research Spotlights Genome Biology ### Microbial WGS using Illumina library prep on the OT-2 A low-cost bacterial isolation and genome sequencing method for characterizing genomic diversity within gut microbiota [Read more ›](https://insights.opentrons.com/hubfs/Applications/NGS/Sanders%202022%20Genome%20Biology.pdf?hsLang=en) BMC Genomics ### Choosing a liquid handler for your genomics lab A review article outlining considerations for genomics labs looking to automate their NGS workflows [Read more ›](https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7576741&blobtype=pdf) ## Resources Explore application data and protocols for different NGS workflow reagents on the OT-2 in the table below. Don’t see your preferred NGS reagents here? Our protocol specialists create protocols for NGS library prep regularly. Book a [virtual demo](https://insights.opentrons.com/schedule-demo?hsLang=en) to discuss your workflow needs with an expert. | Reagent | Application data | Protocols | Verification\* | | --- | --- | --- | --- | | [2S Turbo DNA Library Kit (rebranded as xGEN)](https://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-library-preparation) | [Rapid High Quality Next Generation Sequencing Library Preparation With Swift 2S Turbo DNA Library Kits On The OT-2](https://opentrons-landing-img.s3.amazonaws.com/bundles/swift_automated_ngs_application_note.pdf) | [Swift 2S Turbo DNA Library Kit Protocol: Fully Automated](https://protocols.opentrons.com/protocol/swift-fully-automated) [Swift 2S Turbo DNA Library Kit Protocol: Semi Automated](https://protocols.opentrons.com/protocol/swift-2s-turbo-pt1) | - Opentrons - Partner | | [Omega Bio-tek Mag-Bind TotalPure NGS](https://shop.opentrons.com/omega-biotek-mag-bind-totalpure-ngs-5ml/) | [Fully automated NGS clean up and size selection with Omega Bio-Tek Mag-Bind TotalPure NGS on the OT-2](https://s3.amazonaws.com/opentrons-protocol-library-website/Technical+Notes/Omega_Application_Note.pdf) | [NGS Cleanup and Size Selection with Omega Bio-tek Mag-Bind TotalPure NGS](https://protocols.opentrons.com/protocol/omega_biotek_magbind_totalpure_NGS) | - Opentrons - Partner | | [Illumina DNA Prep Kit](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html) | [Automated library preparation of small genomes using DNA preparation kits](https://insights.opentrons.com/hubfs/App%20Notes/Automating%20DNA%20Library%20Prep%20Illumina%20KAPA%20NEBNext%20App%20Note.pdf?hsLang=en) | Pending | - Opentrons | | [Roche KAPA HyperPrep Kit](https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/integrated-workflow/hypercap.html) | [Automated library preparation of small genomes using DNA preparation kits](https://insights.opentrons.com/hubfs/App%20Notes/Automating%20DNA%20Library%20Prep%20Illumina%20KAPA%20NEBNext%20App%20Note.pdf?hsLang=en) | [Roche HyperPrep](https://protocols.opentrons.com/protocol/sci-roche-hyperprep) | - Opentrons | | [NEBNext Ultra II DNA Library Prep Kit for Illumina](https://www.neb.com/products/e7645-nebnext-ultra-ii-dna-library-prep-kit-for-illumina#Product%20Information) | [Automated library preparation of small genomes using DNA preparation kits](https://insights.opentrons.com/hubfs/App%20Notes/Automating%20DNA%20Library%20Prep%20Illumina%20KAPA%20NEBNext%20App%20Note.pdf?hsLang=en) | [NEBNext Ultra II DNA Library Prep Kit for Illumina](https://protocols.opentrons.com/protocol/sci-neb-next-ultra) | - Opentrons - Partner | | [NEBNext Ultra II FS DNA Library Prep Kit for Illumina](https://www.neb.com/products/e6177-nebnext-ultra-ii-fs-dna-library-prep-with-sample-purification-beads#Product%20Information) | NA | [NEBNext Ultra II FS DNA Library Prep Kit for Illumina (4-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/NEBNext%20Ultra%20II%20FS%20DNA%20Library%20Prep%20Kit%20for%20Illumina%20E6177S%2FL) | - Community | | [NEBNext Ultra II Directional RNA Library Prep Kit for Illumina](https://www.neb.com/products/e7760-nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina#Product%20Information) | NA | [NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (4-part protocol)](https://protocols.opentrons.com/protocol/7805de) | - Community | | [xGen DNA Library Prep MC & EZ Kits](https://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-library-preparation/dna-library-preparation/dna-library-prep-kit) | NA | [IDT xGen MC protocol](https://protocols.opentrons.com/protocol/sci-idt-xgen-mc) [IDT xGen EZ protocol](https://protocols.opentrons.com/protocol/sci-idt-xgen-ez) | - Opentrons | | [Twist Library Preparation Kit](https://www.twistbioscience.com/sites/default/files/resources/2019-09/Protocol_NGS_EnzymaticFragUniversalAdapterSystem_11Sep19_Rev1.pdf) | NA | [Twist library prep (3-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Twist%20Library%20Prep) | - Community | | [Nextera XT DNA Library Preparation Kit](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html) | NA | [Illumina Nextera XT (4-part protocol)](https://protocols.opentrons.com/categories/Featured/NGS%20Library%20Prep%3A%20Illumina%20Nextera%20XT) | - Community | | [AMPure XP](https://www.beckman.com/reagents/genomic/cleanup-and-size-selection/pcr) | NA | [NGS Library Cleanup with AMPure XP Beads](https://protocols.opentrons.com/protocol/70567f) | - Community | | [Illumina DNA Prep with Enrichment Kit](https://support.illumina.com/sequencing/sequencing_kits/illumina-dna-prep-with-enrichment/documentation.html) | NA | [Illumina DNA Prep with Enrichment (2-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Illumina%20DNA%20Prep%20with%20Enrichment) | - Community | | [Zymo-Seq RiboFree ](https://files.zymoresearch.com/protocols/r3000_zymo-seq_ribofree_total_rna_library_kit.pdf)[Total RNA Library Prep](https://files.zymoresearch.com/protocols/r3000_zymo-seq_ribofree_total_rna_library_kit.pdf) | NA | [Zymo RiboFree Total RNA Library Prep (4-part, 2-robot protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Zymo%20RiboFree%E2%84%A2%20Total%20RNA%20Library%20Prep) | - Community | | [EZ DNA Methylation Gold Kits](https://www.zymoresearch.com/collections/ez-dna-methylation-gold-kits) | NA | [EZ DNA Methylation Gold (5-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Zymoresearch%3A%20EZ%20DNA%20Methylation-Gold%20Kit) | - Community | | [Oxford Nanopore Rapid Barcoding Kit](https://store.nanoporetech.com/us/rapid-barcoding-kit.html) | NA | [Oxford Nanopore Ligation Sequencing Kit (2-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Oxford%20Nanopore%20Ligation%20Sequencing%20Kit) | - Community | | [seqWell plexWell LP 384](https://seqwell.com/products/plexwell-lp-384/) | NA | [plexWell LP 384 (4-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/plexWell%20LP384) | - Community | | [Lexogen](https://www.lexogen.com/quantseq-3mrna-sequencing/)[QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina](https://www.lexogen.com/quantseq-3mrna-sequencing/) | NA | [Lexogen ](https://protocols.opentrons.com/protocol/6030b7) [QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina protocol](https://protocols.opentrons.com/protocol/6030b7) | - Community | | [Ion Torrent Oncomine Focus Assay](https://www.thermofisher.com/us/en/home/clinical/preclinical-companion-diagnostic-development/oncomine-oncology/oncomine-focus-assay.html) | NA | [Oncomine Focus Assay (4-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Oncomine%20Focus%20Assay) | - Community | | [Applied Biosystems AgriSeq HTS Library Kit](https://www.thermofisher.com/order/catalog/product/A34144#/A34144) | NA | [AgriSeq HTS Library Kit (4-part protocol)](https://protocols.opentrons.com/protocol/7855ef) | - Community | | [Swift Rapid RNA Library Kit (rebranded as xGEN)](https://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-library-preparation/rna-library-preparation) | NA | [Swift Rapid RNA Library Kit (5-part protocol)](https://protocols.opentrons.com/categories/NGS%20Library%20Prep/Swift%20Rapid%20RNA%20Library%20Kit/) | - Community | | [QIAGEN QIAseq Targeted RNAscan Panels](https://www.qiagen.com/pt/products/discovery-and-translational-research/next-generation-sequencing/rna-sequencing/rna-fusions/qiaseq-targeted-rnascan-panel/?clear=true#orderinginformation) | NA | [QIAseq Targeted RNAscan Panels protocol](https://protocols.opentrons.com/protocol/44b1ac) | - Community | \*Verification categories: Opentrons = has been verified by the Opentrons Team, who verify that the scientific results are as expected. Partner = has been verified by our reagent partner, who verifies that the scientific results are as expected. Community = protocol is in use by members of the Opentrons community. Click Here © OPENTRONS 2026