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See performance parameters and specifications for the MiniSeq System The small footprint allows it to fit seamlessly into laboratoriesThis video provides an overview of overclustering and how it can impact your sequencing data An Illumina Field Applications Scientist shows you how to use SIf someone already owns a MiniSeq, convincing them to buy 2x250 kits is probably easier than convincing them to upgrade to (or expand with) a MiSeq A 2x250 mode on MiniSeq would be projected to yield about 105 gigabases of data, which is actually better than the MiSeq v2 2x250 mode (again, because of higher cluster density)

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Miseq low cluster density-Recorded Webinar (January 21) Illumina nextgeneration sequencing technology allows for massive parallel sequencing Illumina Technical Support invites you to join us for a presentation and discussion on sample preparation, cluster generation and sequencing by synthesis chemistry This webinar is targeted to those new to nextgeneration sequencing and will discuss the following topics Illumina library construction, clusterオーバークラスターしているフローセルのCluster densityは 実際よりも低い数値となる 2) サムネイル画像の確認 推奨最大cluster density/mm2 • MiSeq V2試薬キット 0965k/mm2 V3試薬キット k/mm2 •HiSeq00 k/mm2 •GAIIx k/mm2 原因 オーバークラスター

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Achieving optimal cluster density is critical to highquality sequencing on MiniSeq, MiSeq, NextSeq, and HiSeq 2500 Systems Read more about how to achieve consistent cluster density in order to streamline data outputs Read Bulletin Product Highlights MiSeq Reagent Kits v3 enable the highest output of all MiSeq kits The v3 kits retain the same prefilled, readytouse reagentCluster density and flow cell loading recommendations in Table 1 assume you have a library that's sufficiently diverse If your library is not diverse or sufficiently balanced reduce the library loading amounts recommended in Table 1 by at least 10 % The exact reduction needed depends on several factors such as your library's insert size and whether the first bases of read 1 are · According to Illumina's specifications (Illumina 16b), the recommended cluster density for the mid‐output kit (300 cycles) on the MiniSeq is 170‐2 K/mm 2 Hence, we optimized cluster density by increasing the genetic diversity of the samples for sequencing runs B, C and D, by spiking in an additional Illumina library of genomic DNA from a marine sponge at a

Explore the Illumina workflow, including sequencing by synthesis (SBS) technology, in 3dimensional detail Go from sample preparation, to cluster generationAchieving optimal cluster density is critical to highquality sequencing on MiniSeq™, MiSeq™, NextSeq™ 500/550, and HiSeq™ 2500 Systems On nonpatterned flow cells, cluster density has a significant impact on run performance, specifically data quality and total data outputOverview of how the MiniSeq works, its features, how dual indexing is performed, best practices, and introductory guidance on run analysis View Recorded Webinar Sequencing Optimizing Cluster Density Learn about tips for achieving optimal cluster density View Recorded Webinar × Windows 10 Upgrade Upgrade to MiniSeq Software Suite v2 The MiniSeq system upgrade is

Cluster densities between 0–965 k/mm2 that pass filtering Actual performance may vary based on sample ††The percentage of bases > Q30 is averaged across the entire run, not on a perread or percycle basis bp = base pairs, Mb = megabases, Gb = gigabases, M = millions The information regarding future instrument specifications is intended to outline general product direction and itAchieving optimal cluster density is critical to highquality sequencing on MiniSeq, MiSeq, NextSeq, and HiSeq 2500 Systems Read more about how to achieve consistent cluster density in order to streamline data outputs Read Bulletin Product Highlights NextSeq 500/550 v25 sequencing reagent kits deliver the power of highthroughput sequencing on a benchtop system** Install specifications based on Illumina PhiX control library at supported cluster densities ( k/mm 2 clusters passing filter for v2 chemistry and k/mm 2 clusters passing filter for v3 chemistry) Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter

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MethylMiniSeq Sample Report ZYMO RESEARCH CORP Phone (949) Toll Free (8) 6 Fax (949) services@zymoresearchcom info@zymoresearchcom wwwzymoresearchcom Materials & Methods The samples were processed and analyzed using the Classic RRBS Service Genomewide bisulfite sequencing (Zymo Research, Irvine, CA) DNAMuch higher clustering densities are achieved than with prior patterned flowcells, What I'd really like to see is an update to the MiSeq or MiniSeq that brings 2x higher cluster density and enables more consistent loading/passing filter 50M (100M even better) clusters would be ideal for most of our applications Could this be possible with a patterned flow cell?Density (K/mm 2) The density of clusters on the flowcell (in thousands per mm 2) On MiniSeq, MiSeq, NextSeq and HiSeq 2500 this is an important metric to evaluate if the data are lowquality It should be assessed in tandem with %PF as the two together can diagnose problems with over or underloading your library On HiSeq 4000 and X density is a fixed value and diagnosing issues

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Cluster density is a critically important metric that influences run quality, reads passing filter, Q30 scores, and total data output While underclustering maintains highAchieving optimal cluster density is critical to highquality sequencing on MiniSeq™, MiSeq™, NextSeq™ 500/550, and HiSeq™ 2500 Systems On nonpatterned flow cells, cluster density has a significant impact on run performance, specifically data quality and total data output While underclustering can maintain high data quality, it results in lower data output AlternativelyTotal times include cluster generation, sequencing and base calling on a NextSeq 500 System Install specifications are based on Illumina PhiX control library at supported cluster densities (between 170 and 230 k/mm2 clusters passing filter Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter The percentage of bases >

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Enrichment and sequencing with the MiniSeq Rapid Reagent Kit offers several advantages, including • Sensitive detection of both DNA and RNAbased respiratory pathogens in a single assay in under 24 hours • Comprehensive genome coverage of critical viral pathogens, including SARSCoV2 and Influenza A virus •the common cold (viral rhinitis), sinusitis, pharyngitis, andFOR RESEARCH USE ONLY ILLUMINA PROPRIETARY Part # Rev H March 13 MiSeq® System User Guide · However, it is important to note that random sequencing error, clustering density, percentage of reads passing the filter, and the overall noise in the sequencing signal resulted in 26, 29, and 26 variant calls when comparing the MiSeq run at UCSD and the MiSeq run at Illumina for samples 112, 027, and 066, respectively The WGS results demonstrate the ability to

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PDF In the last decades, methanogenic archaea have been increasingly investigated with regard to their impact on the environment, technological Find, read and cite all the research you needSee performance parameters and specifications for the MiniSeq System The small footprint allows it to fit seamlessly into laboratoriesOn the MiSeq sequencing platform, the optimal raw cluster density specifications for balanced libraries differ by reagent chemistry version • MiSeq v2 reagents accommodate an optimal raw cluster density of 1000–10 K/mm² • MiSeq v3 reagents accommodate an optimal raw cluster density of 10–1400 K/mm²

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Cluster Generation and Sequencing * Install specifications based on Illumina PhiX control library at supported cluster densities (between 129 and 165 k/mm 2 clusters passing filter) Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter All MiniSeq kits are pairedend compatibleLocal Run Manager v2 is available for MiniSeq instruments using MiniSeq Control Software v2 or later, NextSeq 500/550 instruments using NextSeq Control Software v4 and later, and MiSeq instruments using MiSeq Control Software v3 Languages French, Italian, German, Spanish, Chinese (Simplified) min Optimal Cluster Density Best Practices This video discusses optimal cluster densityToday I put on a MiSeq run using Nextera XT library preparation to be run on a V3 600 cartridge After ~ cycles it has given me a low cluster density of 473K/mm2 The quality however is

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Consult the bulletin, Cluster density considerations when migrating Illumina libraries between sequencing platforms for additional information on these variations Additional considerations Insert sizes more than 550 bp are generally not supported on the MiniSeq, NextSeq 500/550, or HiSeq 3000/4000 platforms, and may require additional optimization steps Some applicationsAccording to Illumina's specifications (Illumina 16b), the recommended cluster density for the mid‐output kit (300 cycles) on the MiniSeq is 170‐2 K/mm 2 Hence, we optimized cluster density by increasing the genetic diversity of the samples for sequencing runs B, C and D, by spiking in an additional Illumina library of genomic DNA from a marine sponge at a ratio of 13Library input concentration also has an effect on cluster density and the concentration amount can be different in each lab The usual concentration for optimal cluster density is about 515 pM Library Nucleotide Diversity Library nucleotide diversity is another factor to consider when determining how balanced your library is for the nucleotides in order to achieve maximum

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 · 129 According to Illumina's specifications (Illumina 16), the recommended cluster density for the 130 midoutput kit (300 cycles) on the MiniSeq is 1702 K/mm 2Page 54 Optimally, the cluster density should be 800K/mm² However, a range of 50K– 1300K/mm² is acceptable Clusters Passing Filter (%)—Shows the percentage of clusters passing filter based on the Illumina chastity filter, which measures quality This data appears only after cycle 25 NOTE The chastity of a base call is the ratio of the intensity of the greatest signal divided byYou may need to manually stop and restart RTA if it is stalled or if the network path is down For more information, see the bulletin How to restart RTA on MiSeq system Cluster density is a critically important metric that influences run quality, reads passing filter, Q30 scores, and total data output

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** Install specifications based on Illumina PhiX control library at supported cluster densities ( k/mm 2 clusters passing filter for v2 chemistry and k/mm 2 clusters passing filter for v3 chemistry) Actual performance parameters may vary based on sample type, sample quality, and clusters passing filterThe MiniSeq and NextSeq 500/550 platforms require significantly lower cluster densities than the HiSeq and MiSeq platforms Therefore, it is important to redo cluster density optimization when migrating a library from MiSeq or HiSeq to MiniSeq or NextSeq 500/550 platform and vice versa To or from HiSeq 3000/4000 and NovaSeq 6000Training resources for the MiniSeq System This video discusses optimal cluster density and how over and underclustering can affect your sequencing data It also examines common clustering issues and ways to prevent them 10 min Data Analysis DATE/ LENGTH BaseSpace Sequence Hub Introduction and Analysis Overview Recorded Webinar (May ) llumina

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MiniSeq MiniSeq High/Mid Output 170 –2 MiSeq MiSeq v3 10 –1400 MiSeq v2 1000 –10 NextSeq High/ Mid Output (v25 and v2) 170 2 ※ 上記推奨密度は塩基多様性に偏りのないライブラリーを使用した場合を想定The density of clusters on the flow cell (in thousands per mm 2) On MiniSeq, MiSeq, NextSeq and HiSeq 2500 this is an important metric to evaluate if the data are lowquality It should be assessed in tandem with %PF as the two together can diagnose problems with over or underloading your library On HiSeq 4000 and X density is a fixed value and diagnosing issues with library loadingOptimal Raw Cluster Density HiSeq™ High Output, v3 K/mm 2 High Output, v4 K/mm 2 Rapid Run, v2 K/mm 2 MiSeq™ v2 K/mm 2 v3 K/mm 2 MiniSeq™ Mid and High Output 1702 K/mm 2 NextSeq 500/550™ Mid and High Output 1702 K/mm 2

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 · 1) Reduce your cluster density by 5080% to reduce overlapping clusters 2) Use a high amount of PhiX spike in (up to 50%) of the total library 3) Use custom primers with a random sequence to increase diversity Alternatively, intentionally concatamerize your amplicons and fragment them to increase base diversity at the start of your readsMiniSeq System features – Maximum Output 75 Gb (equivalent to 75 billion bases) within 24 hours – Data quality Quality Score > Q30 (999% accuracy) – Sequencing time when using the HighOutput Reagent Kits 1 x 50 bp in 7 hours (384 samples) 2 x 75 bp in 13 hours (23 samples) 2 x 150 bp in 24 hours (50 smallgenome sequencing samples, 28 targeted amplicon sequencingThe density of clusters for each tile (in thousands per mm2) The number of clusters for each tile (in millions) The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read The percentage of reads from clusters in each tile that aligned to the PhiX

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Local Run Manager is oninstrument analysis software integrated with the system control software Using Local Run Manager, you can record sample information and specify run parameters before starting the run The name assigned to the run appears on the control software run setup screen for faster run setupMiSeq Reagent Kits v2 How to Achieve More Consistent Cluster Density on Illumina Sequencing Platforms Achieving optimal cluster density is critical to highquality sequencing on MiniSeq, MiSeq, NextSeq, and HiSeq 2500 Systems Read more about how to achieve consistent cluster density in order to streamline data outputs

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