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.
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)
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?
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?
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.