Elim Biopharm

Next Gen Sequencing

From HiSeq to MiSeq, Elim has NGS covered. We offer high quality results with some of the fastest turnarounds in the Bay Area.

Elim’s Unprecedented Combination of

Quality, Speed and Cost Advantage

Elim consistently provides high quality, fast turnaround, and cost-effective next generation sequencing services to the life science community. We have expertise in all aspects of next gen sequencing, from platforms and applications to library preparations and bioinformatics. Our customers know that high quality and great turnaround times are Elim’s specialties.

Elim uses advanced platforms like Illumina® and Ion Torrent™ to support your next gen sequencing projects. To ensure consistently high quality sequencing data, we optimize our proprietary protocols and apply stringent QC/QA standards to the entire NGS workflow.

High-Throughput Platforms: Illumina and Ion Torrent
Comprehensive NGS Services: Library Preps, Bioinformatics
Broad Set of Applications

NGS Applications Expertise

Elim has the expertise to support many cutting-edge NGS applications, such as:

  • De novo Sequencing
  • Whole-Genome Resequencing
  • Targeted Sequencing (e.g., Exome Sequencing)
  • Whole-Transcriptome Profiling (e.g., mRNAseq, Tag Profiling)
  • Protein-DNA or Protein-RNA Interactions (e.g., ChIP sequencing)
  • Epigenomics

And Many More… Contact Elim to discuss your next gen sequencing needs.

Comprehensive NGS Services

Elim’s comprehensive NGS service offerings include library preps and target enrichment, quality sequencing and bioinformatics. We have expertise in various library prep and enrichment technologies, including RightOn 1000 Cancer Genes Sequencing, and we deploy leading high-throughput platforms and innovative bioinformatics to meet the most demanding next gen sequencing and applications needs.

Our experienced staffs will work with you from the design stages of your project until you receive and are satisfied with your data. Our customers from leading life science companies and institutes have chosen us for reliable, fast turnaround and high quality NGS services. We have the expertise to help advance your genetic research in the most cost-effective manner. We will work with you to put the power of next gen sequencing in your hands.

illumina® Next Gen Sequencing

Fast Turnaround on High-Throughput Platform

Elim strives to provide the highest quality, fastest turnaround and most cost-effective NGS services. Our comprehensive NGS services include library preps, enrichment, and bioinformatics on the Illumina® platform.

We utilize Illumina® HiSeq and MiSeq to support your NGS needs. The HiSeq 2500 delivers ultra-high-throughput sequencing, and features two run modes to suit different requirements for sequencing data. The Rapid Run mode, with two 2-lane flow cells, can sequence a whole human genome in a day. The High Output Run mode can sequence multiple genomes in a single run, and is well suited for applications that require large amount of data, deep coverage and profiling of complex genomes profiling.

The MiSeq is best suited for small genome sequencing, targeted resequencing, RNA sequencing, library QC, and ChIP-Seq. It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence information. Amplicon sequencing is fast, cost effective and requires only 150 ng of starting gDNA.

ILLUMINA HiSeq 2500 HIGH OUTPUT RUN MODE* RAPID RUN MODE*
Read Length Single Flow Cell (8 Lanes) Dual Flow Cell Run Time Single Flow Cell (2 Lanes) Dual Flow Cell Run Time
1 x 36 47-52 Gb 2 days 9-11 Gb 7 hr
2 × 50 135-150 Gb 5.5 days 25-30 Gb 16 hr
2 x 100 270-300 Gb 11 days 50-60 Gb 27 hr
2 x 150 N/A N/A 75-90 Gb 40 hr
Reads
Passing Filter
Up to 1.5 billion single reads or 3  billion paired-end reads Up to 300 million single reads
or 600 million paired-end reads

To better serve our next generation sequencing customers with the most advanced technology available, Elim-NGS adds Illumina HiSeq v4 sequencing chemistry to our existing HiSeq2500 v3 Rapid and High Output. This sequencing chemistry from Illumina offers improved cluster density and throughput. Each sequencing run can provide our NGS customers higher amount of data with much faster turnaround time.

ILLUMINA HiSeq 2500 HISEQ V4 SPECIFICATIONS TRUSEQ V3 SPECIFICATIONS
Read Length Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time Dual Flow Cell Single Flow Cell Dual Flow Cell Run Time
1 x 36 128-144 Gb 64-72 Gb 29 hrs 95-105 Gb 47-52 Gb 2 days
2 × 50 360-400 Gb 180-200 Gb 2.5 days 270-300 Gb 135-150 Gb 5.5 days
2 x 100 720-800 Gb 360-400 Gb 5 days 540-600 Gb 270-300 Gb 11 days
2 x 125 900-1000 Gb 450-500 Gb 6 days NA NA NA

*HiSeq v4 sequencing chemistry only applied to High Output (eight lanes) runs.

Our high quality NGS data and fast turnaround times attest to our expertise in various high-throughput platforms, applications and sequencing protocols. Contact Elim to discuss your next gen sequencing needs.

 

MiSeq Reagent Kit v2

MiSeq Reagent Kit v3

Read Length

1 × 36 bp

2 × 25 bp

2 × 150 bp

2 × 250 bp

2 × 75 bp

2 × 300 bp

Total Time*

~4 hrs

~5.5 hrs

~24 hrs

~39 hrs

~21 hrs

~56 hrs

Output

540–610 Mb

750–850 Mb

4.5–5.1 Gb

7.5–8.5 Gb

3.3–3.8 Gb

13.2–15 Gb

 

MiSeq Reagent Kit v2 Micro

MiSeq Reagent Kit v2 Nano

Read Length

2 × 150 bp

2 × 250 bp

2 × 150 bp

Total Time*

~19 hrs

~28 hrs

~17 hrs

Output

1.2 Gb

500 Mb

300 Mb

* Total time includes cluster generation, sequencing, and base calling on a MiSeq System enabled with dual-surface scanning.

 

MiSeq Reagent Kit v2

MiSeq Reagent Kit v3

MiSeq Reagent Kit v2 Micro

MiSeq Reagent Kit v2 Nano

Single Reads

12-15 million

22–25 million

4 million

1 million

Paired-End Reads

24–30 million

44–50 million

8 million

2 million

** Install specifications based on Illumina PhiX control library at supported cluster densities (865-965 k/mm2 clusters passing filter for v2 chemistry and 1200-1400 k/mm2 clusters passing filter for v3 chemistry). Actual performance parameters may vary based on sample type, sample quality, and clusters passing filter.

MiSeq Reagent Kit v2 MiSeq Reagent Kit v3
> 90% bases higher than Q30 at 1 × 36 bp > 85% bases higher than Q30 at 2 × 75 bp
> 90% bases higher than Q30 at 2 × 25 bp > 70% bases higher than Q30 at 2 × 300 bp
> 80% bases higher than Q30 at 2 × 150 bp
> 75% bases higher than Q30 at 2 × 250 bp

† A quality score (Q-score) is a prediction of the probability of an error in base calling. The percentage of bases > Q30 is averaged across the entire run.

NGS Applications Expertise

Elim has the expertise to support many cutting-edge NGS applications on the Illumina® platform, including:

De novo Sequencing
Epigenomics
Targeted Sequencing
(e.g., Exome Sequencing)
Whole-Genome
Resequencing
Whole-Transcriptome Profiling
(e.g., mRNAseq, Tag Profiling)
Protein-DNA or Protein-RNA Interactions
(e.g., ChIP sequencing)

And Many More… Contact Elim to discuss your Next Gen Sequencing needs. How NGS works on Illumina® Sequence-by-Synthesis. Learn more in FAQ.

Ion Torrent™ Next Gen Sequencing

Fast Turnaround with Semiconductor Sequencing

Elim is known for high quality, fast turnaround times, and cost-effective NGS services. We provide library preps, enrichment, and bioinformatics as part of our comprehensive NGS services on the Ion Torrent platform.

Elim uses the most advanced Ion Torrent™ sequencers (Ion PGM™ & Ion Proton™) to support your genomic needs. Ion Torrent delivers fast run times and economical sequencing for many applications, including whole genome sequencing of bacteria, viruses and microbial. Ion PGM™ comes with three chip options for different data output speeds. Ion Proton™ can deliver up to 10 Gb of data in a single run, and accelerate exome sequencing when prepped with Ion AmpliSeq™ enrichment technology.

Our entire NGS workflow is optimized to ensure consistently fast turnaround and high quality sequencing data. Contact Elim to discuss your NGS needs.

Ion Torrent™: Output Specifications & Applications

Elim provides exceptional next gen sequencing services for a comprehensive set of applications on the Ion Torrent™ platform.

Ion Torrent™ NGS Ion PGM™
(314, 316, 318 Chips)
Ion Proton™
NGS Service  Turnaround Time 1 day – 1 week;
project dependent
1 day – 1 week;
project dependent
Output per run 200 bases
400 bases
30 MB – 1 Gb
60 MB – 2 Gb
up to 10 Gb
Avg. Read Length 200 & 400 bases up to 200 bases
Avg. Run Time 200 bases
400 bases
2.3 – 4.4 hrs.
3.7 – 7.3 hrs.
2 – 4 hrs.
Number of Reads 400,000 – 5.5 million 60 – 80 million
Applications   • Targeted DNA/ RNA     Sequencing
• Copy Number Analysis
• De novo Microbial     Sequencing
• Bacterial/ Viral Typing
• Metagenomics
• ChIP Sequencing
• Methylation Analysis
• SNP Validation
• Sequencing by     Genotyping
  • Human-Scale Genome     Sequencing
• Exome Sequencing
• Small Genome     Sequencing
• Gene Sequencing
• ChIP Sequencing
• Methylation Analysis
• De novo Sequencing
• Whole transcriptome     Sequencing
• Gene Expression by     Sequencing
• Small RNA Sequencing
Research  Interests   • Cancer Research
• Genetic Disease     Research
• Microbiology
• Stem Cell Research
• Agriculture
• Epigenomics
• Metagenomics
• Forensic Science
• Ancient DNA     Genomics
  • Agricultural research
• Cancer research
• Forensic science
• Stem cell research
• Epigenomics
• Metagenomics
• Ancient DNA genomics

Ordering Elim Next Gen Sequencing

To Submit Your DNA Sequencing Samples

Still waiting in line for your turn in Next Gen Sequencing? Come, try Elim’s next gen sequencing Services, and experience a completely different spirit of speed, reliability, and service.

Whether it is one sample, or a large project, we will work with you to provide the next generation sequencing service that is specific to your needs. Elim’s highly accurate, cost effective, extremely high throughput Next Generation Sequencing is also the natural extension and complementary solution to the conventional capillary DNA Sequencing Services in which we lead and excel. You can count on experiencing the same high quality, worry-free services as other Elim services.

To inquire, obtain quotation, or place order for your specific next gen sequencing needs, please email us. We look forward to working with you!

Next Gen FAQ

Why are you using the Illumina Platform?

After gathering feedback from our customers and reviewing all Next Generation Sequencing platforms, we found that the Illumina platform is the current leader in Next Generation Sequencing. It offers the best combination of data quality and quantity, and is proved to be versatile for a wide variety of genomic applications. However, our goal is to serve your Next Gen Sequencing Needs with the leading technologies available. We are committed to continuously evaluating and adopting the most cutting-edge technologies as they become available.

What kind of projects can I do using NGS Illumina platform?
Please click here to explore the versatility of the Illumina Platform.
What’s the turnaround time for Next Generation Sequencing samples?

Elim offers the fastest turn around for Next Gen Sequencing. The specific time requirement varies depending on the type of the run and length of the read that you require. It can take anywhere from a few days to two weeks. Generally, single-read 36bp runs require a week for data delivery.

Do I have to fill all 8 lanes of the Illumina flow cell to be eligible for an Illumina run?
No. We charge you per lane, and keep in mind that you can have multiple samples run simultaneously in the same lane through multiplexing.
How do I order an Illumina Run?

Please contact us with your specific project needs so that we can design the run with you from the beginning stages.

Also, we like to run one of the lanes as a control to ensure that we are providing you with high quality data, so one full flow cell will have the capability to run 7 lanes of samples.

Do you do library constructions as well?

Yes! Please contact us to discuss your specific project’s needs!

What NGS applications can you support?

Our highly trained staffs have expertise in many NGS applications, including:

De novo Sequencing

Assemble contigs from millions of reads without a reference sequence.

Whole-Genome Resequencing

Discovery of genome-wide changes—copy number variations, chromosomal rearrangements (deletions, insertions, translocations, etc.), and single-nucleotide variations.

Targeted Sequencing (e.g., Exome Sequencing)

Isolation of specific targeted regions of the genome (all coding exons, immunoglobulin switching regions, regions identified by association studies) by long PCR or hybridization to oligonucleotide synthesized on arrays.

Whole-Transcriptome Profiling (e.g., mRNAseq, Tag Profiling)

Sequencing of random-primed cDNA libraries from RNA fractions (nuclear, cytoplasmic, polyA, capped, or small RNA) provides a high-resolution map of all RNA species. Sequencing of tags created by restriction digestion of cDNA generates gene expression profiles with an absolute count (from one to a few million) of the RNA in the sample.

Protein-DNA or Protein-RNA Interactions (e.g., ChIP sequencing)

Discovery of functional transcription factor binding sites across the whole genome and determination of patterns of DNA occupancy by nucleosomes, polymerases, etc. via immunoprecipitation of proteins bound to nucleic acids and the subsequent sequencing of the associated DNA or RNA (ChIP sequencing); selective isolation of DNA via enzyme trapping methods such as trapping of methyltransferases by DNA labeled with aza-nucleotides.

Epigenomics

Determination of DNA methylation variation across the whole genome via bisulfite sequencing or sequencing of fragments generated by methylation restriction polymorphisms, purification of methylated fragments by antibody affinity, or methyltransferase trapping.

And Many More….

How NGS works on Illumina®Sequence-by-Synthesis

Your sample libraries are prepared and annealed to a flow cell. Each flow cell has 8 lanes, so you have the opportunity to run different templates for each lane. The prepared libraries are amplified into millions of clonal clusters, which are then sequenced one base at a time, in parallel, for each of the millions of clusters.

The base calling (sequencing data gathering) steps include incorporation of fluorophore-labeled nucleotides, fluorescence capture of the incorporated nucleotide, and cleavage of the fluorescence molecule. Each of these cycles is run 36, 50, 75, or 100 times, depending on your experimental requirements.

There is also the option to run either single read (only one end of the template clonal clusters will be sequenced) or paired-end read (both ends of the template clonal clusters will be sequenced). A Real Time Analysis program actively interprets the raw data to determine each base being incorporated as the sequence-by-synthesis occurs.

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