Next-Generation Sequencing Reagents and Library Prep Kits

Next-generation sequencing (NGS) reagents and library preparation kits are the consumable inputs that convert nucleic acid samples into sequencer-ready indexed libraries for massively parallel sequencing on Illumina, Oxford Nanopore Technologies (ONT), and Pacific Biosciences platforms - enabling whole-genome sequencing (WGS), RNA-seq, amplicon sequencing, targeted gene panels, whole-exome sequencing (WES), and epigenetic sequencing from a wide range of sample types.

MBP supplies NGS library prep kits from Zymo Research and MagBio - with US order processing in Houston, Texas, and shipping across North America and internationally. Request a quote for NGS reagents and library prep kits for sequencing workflows by contacting customerservice@mbpinc.net.

Next-generation Sequencing (NGS)

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What Is Next-Generation Sequencing?

Next-generation sequencing (NGS), also called high-throughput sequencing or massively parallel sequencing, determines the nucleotide sequence of millions to billions of DNA or RNA fragments simultaneously in a single instrument run. Unlike Sanger sequencing, which reads one locus per reaction, NGS uses sequencing-by-synthesis (Illumina), nanopore translocation (ONT), or single-molecule real-time (SMRT) chemistry (PacBio) to sequence an entire genome, transcriptome, metagenome, or targeted panel in hours to days. Choose NGS reagents based on your sequencing application (DNA-seq vs. RNA-seq vs. amplicon), target platform (Illumina, ONT, or PacBio), sample type (fresh, FFPE, cfDNA, low-input), and throughput requirements.

What you will find out:

NGS Library Preparation Kits: Effective options like the Zymo-Seq SwitchFree series and MagQuant Plus DNA kits, tailored to streamline library production while improving molecular diversity and reducing manual effort.
RNA-sequencing: Customized mRNA and total RNA library kits created for exact gene expression assessments, ensuring precise quantification of low-abundance transcripts with limited starting material.
DNA-sequencing: Trustworthy genomic DNA extraction methods designed for high-yield retrieval and uniform coverage, providing a strong foundation for whole-genome sequencing (WGS) and targeted resequencing projects.

How to Choose NGS Library Prep Reagents

Application type

DNA sequencing applications include whole-genome sequencing (WGS), whole-exome sequencing (WES), targeted gene panels, amplicon sequencing (16S/ITS for microbiome, custom amplicons), and epigenetic sequencing (WGBS, RRBS, ChIP-seq). RNA sequencing applications include mRNA-seq (poly-A enriched), total RNA-seq (rRNA depleted), small RNA-seq (miRNA, piRNA), and single-cell RNA-seq. Each application requires a distinct library prep chemistry and kit format.

Platform compatibility

Confirm library prep kit compatibility with the target sequencing platform before ordering. Illumina-compatible kits are the most common and generate short-read libraries with paired-end 150 bp reads on NovaSeq X, NextSeq 2000, or MiSeq instruments. ONT-compatible kits generate long-read libraries for MinION, GridION, or PromethION. PacBio HiFi kits generate ultra-accurate long reads on the Revio or Sequel IIe. Most Zymo Research NGS library prep kits are optimized for Illumina sequencing.

Sample type and input amount

Standard input amounts are 100 ng-1 microgram of gDNA for WGS, 1-100 ng for targeted panels, and 10-100 ng of total RNA for RNA-seq. Low-input kits support 1-100 pg of total RNA (single-cell or ultra-low input). FFPE-compatible kits use specialized fragmentation and repair chemistry to address formalin-induced crosslinks and DNA damage, accepting inputs as low as 10-50 ng of FFPE-extracted DNA. Confirm the minimum input requirement and the DV200 score threshold for FFPE RNA before selecting a kit.

Zymo Research NGS portfolio at MBP

Zymo Research is a key MBP brand with an NGS library prep portfolio spanning: Zymo-Seq RiboFree Total RNA Library Kit (probe-free rRNA depletion, any organism, 10 ng minimum RNA input, cited in 150+ peer-reviewed studies); Quick-16S Plus NGS Library Prep Kits (normalization-free, 30 minutes hands-on time for 96 samples, V1-V2 or V4 16S rRNA region); Zymo-Seq RRBS Library Kit (reduced representation bisulfite sequencing, as little as 2 hours hands-on time); and Zymo-Seq UDI Primer Sets (unique dual index barcodes for multiplexed sequencing). Zymo Research kits are cited extensively in published microbiome, transcriptomics, and epigenomics research.

Automation compatibility

High-throughput genomics cores and biobanks processing hundreds of samples per week benefit from automation-compatible library prep formats. Zymo Research Quick-16S Plus kits are 100% automation ready and require no normalization step between PCR and pooling. Assess liquid-handling robot compatibility (Hamilton, Beckman, Tecan, Agilent Bravo) with the kit vendor before scaling.

Specifications Context

NGS library quality is assessed by three metrics: concentration (Qubit fluorometry; target 2-10 nM for Illumina clustering), fragment size distribution (Bioanalyzer or TapeStation; target 300-500 bp insert for standard Illumina), and library complexity (assessed by PhiX spike-in error rate and percentage of duplicate reads). Adapter dimer contamination below 5% of total library molecules is recommended before sequencing; size selection with SPRI beads (such as AMPure XP, 0.8-1.0X bead ratio) removes dimers efficiently. PCR-free WGS library preparation is increasingly preferred for high-coverage sequencing to eliminate PCR amplification bias, particularly in GC-rich and AT-rich regions, and requires a minimum input of 200-500 ng of high-molecular-weight DNA (HMW gDNA).

Boost your genomic knowledge—contact the MBP team today for a quote on our specialized NGS preparation services.

FAQ

Next-generation sequencing (NGS) is a massively parallel sequencing technology that determines the nucleotide sequence of millions to billions of DNA or RNA fragments simultaneously in a single run. The process begins with library preparation -- fragmenting nucleic acids, ligating indexed adapters, and amplifying the library -- followed by sequencing on an instrument (Illumina, Oxford Nanopore, PacBio) that reads each fragment. Data is then assembled and analyzed bioinformatically. A single Illumina NovaSeq X run generates up to 16 billion 150 bp reads, enough to sequence over 60 human genomes at 30x coverage.

NGS library preparation typically involves six steps: (1) nucleic acid extraction and QC to confirm concentration (Qubit) and integrity (Bioanalyzer/TapeStation); (2) fragmentation of DNA by sonication, enzymatic cleavage, or transposase-based tagmentation, or RNA fragmentation followed by cDNA synthesis; (3) end-repair and A-tailing to generate blunt, 5'-phosphorylated, 3'-dA-tailed fragments; (4) adapter ligation to add platform-specific sequences and sample index barcodes; (5) size selection using SPRI beads to remove adapter dimers; and (6) PCR amplification to enrich ligated fragments and complete dual indexing.

Whole-genome sequencing (WGS) sequences the entire genome including coding and non-coding regions, detecting SNVs, indels, copy number variants, and structural variants across the full genomic sequence. Whole-exome sequencing (WES) uses hybridization-capture probes to enrich the protein-coding exons, which represent 1-2% of the genome but harbor approximately 85% of known disease-causing mutations. Targeted sequencing uses PCR amplicons or probe capture to sequence a defined gene panel at very high depth (500x-10,000x), enabling detection of low-frequency variants in clinical oncology, infectious disease, and pharmacogenomics research.

MBP supplies Zymo Research NGS library prep kits including the Zymo-Seq RiboFree Total RNA Library Kit for total RNA-seq with probe-free rRNA depletion from any organism, Quick-16S Plus NGS Library Prep Kits (V1-V2 and V4 regions) for microbiome 16S amplicon sequencing with 30 minutes of hands-on time for 96 samples, the Zymo-Seq RRBS Library Kit for reduced representation bisulfite sequencing, and Zymo-Seq UDI Primer Sets for multiplexed library indexing. Contact MBP to confirm current catalog availability and request quotes for multi-kit orders.

NGS library quality is assessed by three measurements: (1) concentration using a fluorometric method such as Qubit dsDNA HS Assay, targeting 2-10 nM for Illumina; (2) fragment size distribution using an Agilent Bioanalyzer (DNA 1000 or High Sensitivity DNA chip) or TapeStation (D1000 ScreenTape), with a target average insert of 300-500 bp for standard paired-end Illumina runs; and (3) adapter dimer content, which should be below 5% by molar fraction before loading. Libraries failing size or concentration thresholds should be re-size-selected with SPRI beads or re-quantified before pooling.

Minimum input depends on the kit: standard total RNA-seq kits (including Zymo-Seq RiboFree) accept 10 ng-1 microgram of total RNA. Low-input RNA-seq kits (poly-A enrichment based) accept 5-25 ng of total RNA. Ultra-low-input kits using SMART-Seq chemistry accept 10 pg-5 ng of total RNA, including single-cell amounts. FFPE RNA input requirements are governed by DV200 (percentage of RNA fragments above 200 nucleotides); samples with DV200 above 30% can typically be processed with FFPE-optimized kits. Confirm input range and DV200 threshold in the specific kit's protocol before extraction.

PCR-free library preparation omits the amplification step after adapter ligation, avoiding PCR-induced amplification bias that causes uneven coverage in GC-rich regions (over-represented) and AT-rich regions (under-represented). PCR-free WGS libraries require higher input (200-500 ng of high-molecular-weight gDNA) to compensate for the absence of enrichment. PCR-free prep is preferred for high-coverage (30x or greater) WGS, allele frequency studies, copy number variation analysis, and structural variant detection where uniform genome coverage is critical. At lower coverage or with limited input, PCR-based libraries with a high-fidelity polymerase are standard.

MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center, and supports institutional purchase order procurement for NGS library prep kits and supporting reagents. Genomics core facilities, biobanks, and academic labs can contact MBP to establish vendor status, request quotes for multi-kit orders, or set up repeat purchasing agreements for ongoing sequencing programs. Submit inquiries via the Quick Order portal at mbpinc.net or contact MBP directly for pricing on Zymo Research and Eurofins Genomics sequencing products.

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