Base Calling


Base calling is the process by which an order of nucleotides in a template is inferred during a sequencing reaction. Next generation sequencing platforms that use fluorescently labeled reversible terminators have a unqiue color for each base. These are incorporated into the complementary strand of the DNA template and captured with a sensitive CCD camera. These images are processed into signals which are used to infer the order of nucleotides, also known as base calling. While sequencing platforms typically have integrated base calling software, the development of high performing base calling algorithms is an area of ongoing research.

Base calling accuracy is typically measured by a Q score (Phred quality score), a common metric to assess the accuracy of a sequencing run. Q scores are defined as logarithmically related to base calling error probability.

Q = - 10 log P / log 10

If a sequencing run is assigned a Q score of 40, this is equal to the probability of an incorrect base call of 1 in 10,000 times, or 99.99% base calling accuracy.

Q Score 10 - Base calling accuracy 1 in 10 - Probability of incorrect base 90%

Q Score 20 - Base calling accuracy 1 in 100 - Probability of incorrect base 99%

Q Score 30 - Base calling accuracy 1 in 1,000 - Probability of incorrect base 99.9%

Q Score 40 - Base calling accuracy 1 in 10,000 - Probability of incorrect base 99.99%

Q Score 50 - Base calling accuracy 1 in 100,000 - Probability of incorrect base 99.999%

A lower Q score of 10 means, there is the probability of an incorrect call in 1 of 10 bases. Lower Q scores can lead to increases in false positive variant calls and reduces the overall confidence an investigator has in their sequencing data.

Providers offering Base Calling (found 20)


Parseq Lab

Czechia

Parseq Lab is experienced in: - massively parallel sequencing data analysis - client-tailored algorithms and software development - analysis pipelines deployment

We offer: - whole genome/exome and targeted sequencing data analysis - de novo assembly - SGV detection and annotation - expression analyses - metagenomics analysis - transcriptomics analysis - proteomics research - genuine task-specific workflows design - custom bioinformatics applications development - statistical data analysis

Collaborations: genomic research labs, sequencing facilities, academic and research institutions.

Years in service: 13

Other services offered by Parseq Lab:

Service Description Price

KCCG Sequencing Laboratory, Garvan Institute of Medical Research

NGS provider Australia

For more than 50 years, the Garvan Institute of Medical Research has led scientific discovery and pioneered insights in the areas of cancer, metabolic, neurological, immunological and bone disease.

We were one of the first sites in the world to acquire the Illumina HiSeq X Ten sequencing platform, which provides the opportunity for low cost and large scale whole human genome sequencing.

Garvan was uniquely positioned to leverage its advanced sequencing infrastructure, comprehensive computational architecture, innovative data analysis and archiving solutions. Garvan has become a world-leading hub of expertise in generation, analysis, interpretation and application of genomic data.

The laboratory operates with a dual purpose; • providing the global research community access to best-in-class WGS technology and data analysis • offering Australia’s first accredited (ISO 15189) WGS-based pathology service to the clinical community

We have sequenced and delivered >16,000 human and non-human genomes on the X Ten platform to date and have the capacity to run ~1200 genomes per month. Please see below for our deliverables for this service:

Deliverables • Clinically accredited laboratory (ISO 15189) • Human and non-human whole genome sequencing • TruSeq Nano DNA or PCR-Free library preparation • Includes DNA and library QC • Flexible choice of 15x (TruSeq Nano) or 30x coverage for human DNA (as defined by Illumina^) • Flexible choice of ≥50Gb (TruSeq Nano) or ≥100 Gb raw data • 150bp paired-end read length • ≥75% bases above Q30 • Delivery of FASTQ data via online portal DNAnexus with clinical-grade security and privacy

Options • Precision FDA award-winning bioinformatics analysis using gold-standard alignment software GATK and variant calling software BWA to generate best practice BAM and VCF files • Hard drive delivery

^ in line with Illumina’s ‘Sequencing Coverage Calculation Methods for Human WGS’ documentation

Years in service: 12

Other services offered by KCCG Sequencing Laboratory, Garvan Institute of Medical Research:

Service Description Price
Other Services Precision FDA award-winning bioinformatics analysis using gold-standard alignment software GATK and variant calling software BWA to generate best practice BAM and VCF files Our team achieved the highest overall precision in detecting SNPs in the unknown genome, in an international competition designed to test the performance of genome informatics pipelines worldwide. The team’s precision level o… $275.00 USD (per sample)

AC-Gen Reading Life S.L.

NGS provider Spain

AC-Gen Reading Life is a Spanish pioneer company in the application of Next-Generation Sequencing technology (NGS) for clinical use. We have the NGS Ion Torrent™ platform available in our lab, and can carry out data analysis. Ion Torrent™ technology for NGS is the fastest and cost effective technology in the market for DNA analysis.

Mission: to improve the health and quality of life of people affected by genetic diseases.

Objectives: To provide high quality genetic analysis and cost-effective to help the implementation of personalized genomic medicine, as well as foster the development of partnerships in the field of research.

Years in service: 11

Other services offered by AC-Gen Reading Life S.L.:

Service Description Price
Targeted Capture Analysis Base calling, annottation $300.00 USD (per sample)
Genome Annotation Bacteria genome $400.00 USD (per sample)
Base Calling Torrent server and Ion reporter $300.00 USD (per sample)

Igenbio, Inc.

United States of America

Expertise:

Igenbio, Inc. develops genome analysis products and services for the life science industry. Our scientists have broad experience in both in silico and wet lab sequencing, research and development with more than 100 relevant publications in these areas. Igenbio has a proven track record of delivering scientific results for academic, governmental, and industrial institutions for two decades.

Our expertise includes, but is not limited to:

  • Whole Genome Sequencing
  • RNA-Sequencing
  • Metatranscriptomics Sequencing
  • Metagenome Sequencing
  • Common and custom amplicon sequencing
  • Genome Assembly & Annotation
  • RNA-Seq Analysis
  • Amplicon Sequencing Analysis
  • Metagenome Analysis
  • Genome ORF calling: Eukaryotes and Prokaryote Genomes
  • Pathway Analysis
  • Metabolic Reconstruction
  • SNP Discovery & Analysis
  • Comparative Genomics
  • Available for all organisms, including humans, animals, plants, bacteria, and viruses.
  • Haploid, diploid or polyploid assemblies

Infrastructure:

Igenbio has a large, secure cloud infrastructure that can expand to meet any project demands you may have - from large number of samples to quick turnaround times. Please inquire for more information.

At Igenbio, Inc. security of your data is a top priority. Your data is protected by best practices in physical and data security measures. This includes 24/7 physical security and monitoring, and the best available encryption for storage and transmission. Our employees are trained and knowledgeable in data security best practices.

Years in service: 11

Other services offered by Igenbio, Inc.:

Service Description Price
Differential Gene Expression Analysis Inquire
Comparative Genome Analysis Inquire
Metagenomic Analysis - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 and Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva,… Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Gene Annotation and Functional Assignments placing genes into their functional or metabolic context utilizing KEGG Pathways, Gene Ontology, and the ERGO database. Optional - Identification of Antibiotic Resistance - including the genes, pathways, and specific drugs Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly All current sequencing technologies support - Illumina, PacBio, Oxford Nanopore, 10x, Hi-C, Ion Torrent, and others. Igenbio scientists utilize a multitude of assembly strategies - denovo, reference based, hybrid, metagenomic, and others. Inquire
Base Calling Inquire
Microbiome Analysis - Quality analytics of sequence reads - State of the art sample processing using academically-proven tools such as DADA2 or Kraken2 that work on all sequencing platforms such as Illumina & Pacific Biosciences. - Fast and accurate taxa identification using state-of-the-art machine learning algorithms that can identify taxa down to the species level. - Supports public databases (such as Silva, Gree… Inquire

Genotypic Technology

NGS provider India

Genotypic Technology is the first genomics company based in India with a state-of-the-art, ISO 9001:2008 accredited, SAP-enabled, 12,000 square feet facility in Bangalore. Our high-throughput facility enables us to offer customized services for experiment design consultation, protocol optimization, microarray and probe designing, next-generation sequencing (NGS), and bioinformatics solutions to clients from academia, biotech, and pharma sectors worldwide.

We have been providing high-quality sequencing services, including whole-genome sequencing (WGS), transcriptome sequencing, shotgun metagenome sequencing, and de-novo assembly since 2000. Our skilled team has experience in working with genomes of all sizes and nucleic acids from various sources on Illumina, Oxford Nanopore, and other platforms. We have developed targeted panels for various viruses like Adenovirus, KFDV, SARS-CoV-2, Dengue, and pipelines for predicting virulent strains that may be difficult to treat with conventional antibiotics.

Our broad range of metagenome services includes targeted and whole-genome metagenome and metatranscriptome sequencing. Our long amplicon metagenome approach provides the best resolution of microbes up to the sub-species level, while whole-genome metagenome sequencing enables the identification of gene clusters, resistome, and novel pathways in a given environment. We also specialize in Ribo-footprinting and RNA immunoprecipitation sequencing, ChIP sequencing, and targeted methylation sequencing.

Years in service: 26

Other services offered by Genotypic Technology:

Service Description Price
Differential Gene Expression Analysis Differential Gene expressions, SNP variants and annotations with known reference, SSR discovery $69.00 USD (per sample)
Transcriptome Mapping $25.00 USD (per sample)
Custom scripting and special projects Bioinformatics support for 1 day - includes skype/webex consultation with detailed report. 120.00
Read Filtering and Cleaning $2.00 USD (per sample)
Exome Analysis Exome analysis - from raw data to VCF files and annotations from dbSNP, 1000 genome, COSMIC, SIFT, Polyphen2 and more $45.00 USD (per sample)
ChIP-Seq Analysis $250.00 USD (per sample)
Metagenomic Analysis $25.00 USD (per sample)
Transcriptome de novo Assembly Denovo transcriptome assembly with differential gene expression values. $600.00 USD (per sample)
Whole Genome de novo Assembly $2900.00 USD (per sample)
Base Calling $20.00 USD (per hour)

Diagnomics

United States of America

Diagnomics Inc. is a biotech company in the heart of the Biotech Beach, in San Diego California. The company focuses on products and services for personalized medicine based on personal genome and cutting edge bioinformatics analysis. Diagnomics provides complete personal genome sequencing and bioinformatics solutions to biomedical researchers, physicians and individuals seeking to understand the genetic influence of personal health and disease.

Expertise:

We aim to provide the highest possible quality genome sequencing service and annotation solutions from next generation sequencing (NGS) technology to guide personalized medicine based on an individuals' genetic information.

Infrastructure:

We are taking high-throughput computation and informatics seriously, and are constantly upgrading our server farm and softwares to enable cutting-edge bioinformatics for state-of-the-art genomic analysis. To that end, we house our infrastructure at a world class data center. Our server farm is located in San Diego, California at the ScaleMatrix facility.

Other services offered by Diagnomics:

Service Description Price
SNP / Indel Mapping Inquire
SNP / Indel Calling Inquire
Targeted Capture Analysis Inquire
Genome Annotation Inquire
Variant Annotation Inquire
Base Calling Inquire

EarlyDx

NGS provider

EarlyDx is committed to providing cutting-edge non-invasive genomics technologies and best-in-class early disease diagnostics. Our proprietary cfDNA-based technologies, in combination with powerful AI algorithms, have shown great potential to transform non-invasive biomarker discovery, diagnostics, and precision medicine for almost any diseases, including cancers, aging, metabolic diseases, autoimmune diseases, imprinting diseases, and neurological diseases.

Our key cfDNA-based best-in-class technologies include:

  1. cfMethyl-seq: a powerful and cost-effective NGS solution to profile the cfDNA methylome
  2. cfSNV: a cutting-edge computational tool to accurately call mutations directly from blood
  3. cfTrack: for non-invasive monitoring of cancer MRD, recurrence, and evolution
  4. EarlyDx-Cloud: a comprehensive bioinformatics data analysis platform for liquid biopsy

Please check out our relevant publications in details: https://earlydx.com/technologies/publications/

Years in service: 2

Other services offered by EarlyDx:

Service Description Price

Genevia Technologies

Finland

Genevia Technologies provides a wide range of microarray and next generation sequencing data analyses, and bioinformatics services to life science companies and academia. In addition, we offer bioinformatics consulting projects at a fixed price, and genome-wide experiments done in collaboration with the top service providers.

Expertise:

Our expertise is in handling multiple microarray (expression, copy number, ChIP, methylation, etc) and next-gen sequencing (DNA-seq, RNA-seq, MeDIP-seq, ChIP-seq, GRO-seq, etc) data simultaneously and effectively, and combining them with other data such as clinical variables or pathway information. We have experience in most common mammalian systems, but especially in multiple human cancers. We have also worked on data from multiple species of lower eucaryotes and bacteria.

Infrastructure:

We have access to dedicated file storage servers, a computing cluster, a computing grid (of over 1000 CPUs), and cloud computing capabilities.

Visit our homepage to read more about us and our bioinformatics as a service: www.genevia.fi

Other services offered by Genevia Technologies:

Service Description Price
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Read Filtering and Cleaning Inquire
ChIP-Seq Analysis Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Targeted Capture Analysis Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Base Calling Inquire

Next Generation Intelligence

NGS provider Italy

NGI is a platform for Next Generation Sequencing data analysis. We offer a wide range of bioinformatics tools and an experienced and professional collaboration service for any type of biological data analysis. We provide both standard and customized analysis, custom softwares and pipelines development and post-sequencing support. We'll enhance and make easier your discovery process.

Expertise:

Our expertise is in the epigenetics field in mouse and human organisms.

Infrastructure:

we will provide FTP access to our storage server to upload raw data and download analyzed data.

Other services offered by Next Generation Intelligence:

Service Description Price
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Read Filtering and Cleaning Inquire
Exome Analysis Inquire
ChIP-Seq Analysis Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Targeted Capture Analysis Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Base Calling Inquire

The Africa Genomics Centre and Consultancy (TAGCC) ltd

Kenya

TAGCC is an African company offering services in next generation sequence data analysis and consultancy in genomics. We have implemented a wide range of pipelines to analyse NGS data from various platforms including Illumina and 454. We support design and implementation of genomics and NGS based projects.

Years in service: 10

Other services offered by The Africa Genomics Centre and Consultancy (TAGCC) ltd:

Service Description Price
Differential Gene Expression Analysis We Identify differentially expressed and significant genes from RNA-seq data. Our workflow includes QC clean up, removal of ribosomal RNA contamination followed by denovo or reference based mapping. RPKM/FPKM-based quantitation. $80.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $110.00 USD (per sample)
Other Services Admixture modelling and SNP phylogenetics. Use genetic data to infer the structure and evolutionary history of populations (Time is dependent on VCF/PED file size) $225.00 USD (per hour)
Read Filtering and Cleaning QC analysis, trimming and low quality reads removal. Both Raw and QC trimmed Fastq files will be made available. $24.00 USD (per sample)
Exome Analysis We analyse full exomes from raw sequence data through the process of cleaning, alignment, variant calling to analysis ready vcf file with variants effects summary. $125.00 USD (per sample)
SNP / Indel Mapping Map SNPs and Indels. $110.00 USD (per sample)
Genome Mapping Alignment of NGS data to reference genome and generate mapping statistics $60.00 USD (per sample)
Metagenomic Analysis Generating publication ready Phylogenetic trees, Alpha and beta-diversity, rarefactions, rank abundance plots, relative abundance bar plots, with integration of meta-data, etc. Inquire
SNP / Indel Calling Identify and qualify SNPs and Indels. $110.00 USD (per sample)
Base Calling Demultiplex data and convert BCL or SFF files to FASTQ files. (Time is dependent on file size) $120.00 USD (per hour)

STAB VIDA

NGS provider Portugal

Years in service: 12

Other services offered by STAB VIDA:

Service Description Price
Differential Gene Expression Analysis Deliverables include the raw data fastq seq files, transcriptome mapping, gene expression analysis and a report (including Q score, number of reads, coverage, etc) $200.00 USD (per sample)
SNP / Indel Mapping Deliverables include the raw data fastq seq files, consensus sequence, list of genetic variants and a report (including Q score, number of reads, coverage, etc) $200.00 USD (per sample)
Genome Mapping Deliverables include the raw data fastq seq files, consensus sequence and a report (including Q score, number of reads, coverage, etc) $200.00 USD (per sample)
Whole Genome de novo Assembly Deliverables include the raw data fastq seq files, list of contigs and a report with results (including Q score, number of reads, coverage etc) $200.00 USD (per sample)
Base Calling Deliverables include the raw data fastq seq files Inquire

NXT-Dx

NGS provider Belgium

At NXT-Dx we can offer SE50, PE50 and PE100 sequencing on the Illumina HiSeq. On top of this we can also offer different sequencing settings on the Illumina MiSeq and shortly we will also be able to offer sequencing on the Illumina NextSeq.

We can offer sequencing of already prepared libraries but we can also offer full-scope projects whereby we receive cells, tissue, gDNA or RNA and take care of the sample preparation, library prep, sequencing and bio-informatics analysis.

We have worked with samples from all kind of species (mammalian, plant, bacterial) and all kind of cell types.

We pride ourselves in having close contact with our customers and only one single contact point. Also after the delivery of the data, we remain available to answer any questions customers might have on their data, their analysis, etc.

Years in service: 13

Other services offered by NXT-Dx:

Service Description Price
Differential Gene Expression Analysis $170.00 USD (per hour)
Transcriptome Mapping $170.00 USD (per hour)
Comparative Genome Analysis $170.00 USD (per hour)
Custom scripting and special projects $170.00 USD (per hour)
Read Filtering and Cleaning $170.00 USD (per hour)
Exome Analysis $170.00 USD (per hour)
ChIP-Seq Analysis $170.00 USD (per hour)
Small RNA Mapping $170.00 USD (per hour)
Genome Mapping $170.00 USD (per hour)
Targeted Capture Analysis $170.00 USD (per hour)
Genome Annotation $170.00 USD (per hour)
Small RNA Annotation $170.00 USD (per hour)
Methylation Analysis $170.00 USD (per hour)
Transcriptome Annotation $170.00 USD (per hour)
Variant Annotation $170.00 USD (per hour)
Base Calling $170.00 USD (per hour)

SciBerg

Germany

We offer computational analyses of Next-Generation Sequencing data (Illumina and Ion Torrent platforms), including RNA-seq, small RNA-seq, DNA-seq, Bisulfite-seq and ChIP-seq. Our bioinformatics support can be fully customized for your research needs, the scope and objectives of the study. We apply only up-to-data well-proven software and pipelines working under Unix/Linux environment. Optionally, our experts can help to interpret the obtained results from the scientific point of view, provided some of them are working in a close research field.

Other services offered by SciBerg:

Service Description Price

Omega Bioservices

NGS provider United States of America

Our facility is unique because we offer the full range of NGS service from sample extraction through to data analysis. Sample extraction capabilities and expertise cover the entire spectrum of both environmental and clinical sample types.

Years in service: 12

Other services offered by Omega Bioservices:

Service Description Price
Differential Gene Expression Analysis Identify differentially expressed genes among samples using RNA-seq technique. Human, mouse, rat, fruit fly, cattle, pig, chicken, zebrafish, C. elegans, maize, thale cress, Japonica rice (Oryza sativa) and yeast, up to 7.5gb/sample. $56.00 USD (per sample)
Differential Gene Expression Analysis Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. $110.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $332.00 USD (per sample)
Custom scripting and special projects We provide study specific bioinformatics analysis (known as tertiary analysis). such as (not limited to) 1) process secondary sequencing data analysis for a variety of platforms such as Nanostring, Nanopore, single cell expression. 2) integrative analysis across sequencing platforms (such as DNA-seq, RNA-seq, Chip-seq) 3) integrate meta/clinical information, perform association study and build p… $60.00 USD (per hour)
Read Filtering and Cleaning Examination of sequencing quality and removal of low quality reads prior to downstream analysis provided free of charge with sequencing service if desired. $110.00 USD (per sample)
Exome Analysis Whole exome sequencing involves capturing the coding region of the genome, or exons (EXpressed regiONS). SNVs and indels are the most important and abundant types of variation in exons. Human exome analysis provided free of charge with sequencing service. $332.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq is a technique to identify DNA loci bound by a specific protein. The standard output of ChIP-seq analysis includes peak call and motif enrichment at binidng sites. $332.00 USD (per sample)
Small RNA Mapping Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $221.00 USD (per sample)
SNP / Indel Mapping Mapped to the reference genome and annotated using public database. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Mapping Genome mapping is a technique used to assign the location of a particular gene on a chromosome and measure their relative locations and distances between genes. Mapping to many model organisms provided free of charge with sequencing service. $110.00 USD (per sample)
Metagenomic Analysis Metagenomic analysis involves the identification and quantification of genetic material from environmental, uncultured microorganisms. Analysis involving only 16S rRNA amplicon sequences are provided free of charge with sequencing service. $551.00 USD (per sample)
SNP / Indel Calling Identify SNPs and Indels in the region of interested, using DNA sequencing. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
SNP/SV/CNV Discovery Variants discovery. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Targeted Capture Analysis Variant call, gene annotation. Provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Annotation Annotation is the process by which pertinent information about these raw DNA sequences is added to the genome databases. This involves describing different regions of the sequence and identifying which regions can be called genes. $221.00 USD (per sample)
Small RNA Annotation Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $332.00 USD (per sample)
Methylation Analysis The processing of bisulfite sequencing data includes sequence alignment and the quantification of absolute DNA methylation at base resolution. Methylation analysis for data generated from the Illumina TruSeq kit are provided free of charge with sequencing service. $553.00 USD (per sample)
Transcriptome de novo Assembly Identify and quantify putative mRNA transcripts using RNA-seq data for unannotated species. $553.00 USD (per sample)
Transcriptome Annotation Annotate or predict functions of transcribed genes using well know gene ontology tools. $332.00 USD (per sample)
Variant Annotation Identified variants will be mapped to the reference genome and annotated using public database. Analysis for human sequences provided free of charge with sequencing service. $332.00 USD (per sample)
Whole Genome de novo Assembly Prices vary according to genome type. Please contact our Science Project Team. Some small genome assembly provided free of charge with sequencing service. $3315.00 USD (per sample)
Base Calling Demultiplex data and convert BCL files to FASTQ files $110.00 USD (per sample)

One Health Innovation Lab

NGS provider United States of America

At the forefront of scientific advancement, our sequencing and biorepository facility is part of the One Health Shared Services at Innovation Foundation dedicated to enhancing the health and well-being of humans, animals, and ecosystems.

Our mission: To advance health across boundaries.

Sequencing platforms: NextSeq2000: Versatile Illumina platform for flexibility and speed. MiniSeq: Compact and cost-effective, suitable for targeted sequencing and small-scale applications.

We offer cutting-edge genomic research services & Bioinformatics support. Bioinformatics Support: Our bioinformatics experts collaborate closely with you.

Why Choose Us? Accuracy: Our cutting-edge technology ensures reliable results. Fast Turnaround: Get your data quickly without compromising quality. Expert Support: Our scientists are here to assist you. Custom Solutions: Tailored services to meet your specific research goals. End-to-end solutions: From experimental design to data analysis, we guide you every step of the way.

Contact Us at OHIL@okstate.edu to discuss your sequencing needs or possible collaborations with the One Health Innovation Lab.

Other services offered by One Health Innovation Lab:

Service Description Price
Differential Gene Expression Analysis Differential Gene Expression Analysis from RNAseq data. Input - gene counts from RNAseq (output from Transcriptome Mapping) Deliverables - PCA plot showing sample clustering, MA plot (log2 fold changes in gene expression between groups with significant calls highlighted), list of Differentially Expressed Genes (DEGs), GSEA or GO Analysis on DEGs Note: Price advertised is per biological compar… $50.00 USD (per sample)
Transcriptome Mapping Alignment of RNAseq data to the reference genome, removal of PCR duplicates, report of alignment statistics with gene counts. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, gene counts $50.00 USD (per sample)
Custom scripting and special projects Custom scripting or analysis, data visualization assistance, and additional services are available starting around $20 per sample. Please reach out to us to get a more accurate quote - we'd love to help you with your project! $20.00 USD (per sample)
Exome Analysis Analysis of targeted exome sequencing. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, exome panel coverage stats $50.00 USD (per sample)
Genome Mapping FOR WHOLE GENOME SEQUENCING ALIGNMENT ONLY. Includes alignment of .fastq file to reference genome, removal of PCR duplicates, and report of alignment quality. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats $150.00 USD (per sample)
Genome Mapping FOR TARGETED AMPLICON SEQUENCING ALIGNMENT ONLY. Includes alignment of .fastq file to reference genome, removal of PCR duplicates, and report of alignment quality. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats $50.00 USD (per sample)
SNP/SV/CNV Discovery Variant calling analysis on aligned genomic data. Input - .bam file (alignment) Deliverables - .vcf file of variants $20.00 USD (per sample)
Targeted Capture Analysis For data types such as ChIPseq, ATACseq, CUT and RUN, etc, in which amplicons are targeted for sequencing. Includes alignment to the reference genome, removal of PCR duplicates, a report of alignment quality, and calling of "peaks"/"binding sites". Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, binding site/"peak" calls (w/ and w/o … $50.00 USD (per sample)
Base Calling Base calling from .bcl file. Input - .bcl file Deliverables - fastq file and fastqc report $20.00 USD (per sample)

Wyzer Biosciences

NGS provider United States of America

Privately held, Wyzer Biosciences, Inc. was founded in 2011 and is located in dynamic Cambridge, MA, the home of Harvard, MIT and many other world-class educational and biotech institutions. Through our expertise in molecular biology we provide services to our partners and collaborators in industry and academia that will aid them in their ongoing research. Currently we are focusing on providing the Sanger, NGS (Illumina, Complete Genomics), Third-Generation (Nanopore) DNA sequencing and DNA prep services. Our company is ideally suited to solve your simple and complex sequencing needs. Over the years we have perfected all stages of Sanger sequencing workflow and are particularly well-equipped to deal with many types of difficult templates. Our strength is in fast and reliable double-strand sequence finishing, which includes primer design, contig assembly with editing and rudimentary data analysis. We provide inexpensive plasmid confirmation sequencing service that may be run on one or two platforms to get though difficult motifs and provide high quality data for the entire molecule. We provide various one-of-a-kind services along with the standard sequencing services. Our NGS and TGS services may include secondary bioinformatics analysis like data alignment to references and generation of consensus sequences. If you have some unique sequencing needs on small and medium scale, ask us. We will do our best to accommodate you. In the future we plan to expand our services and offer even wider choice of sequencing platforms and processes to better suit our customer’s needs.

Years in service: 14

Other services offered by Wyzer Biosciences:

Service Description Price
Metagenomic Analysis Minimum Units: 1 Hour $300.00 USD (per hour)

CD Genomics

NGS provider United States of America

We specialize in the services of DNA sequencing, genotyping, DNA library construction and aptamer development. Shotgun Library Sequencing, cDNA Library Sequencing, SAGE Library Sequencing, Whole Genome Sequencing and Primer Walking Sequencing. we offer high quality Re-sequencing & SNP Discovery Services. Quite a few of our staff scientists once participated in the International HapMap Project too.

extensive experience in whole genome shotgun sequencing services. Beginning from bacterial cells or genomic DNA, we provide you with accurate genome consensus sequences. We are also experienced in genome annotation and comparative genomics research. Notably our staff scientists have finished a number of whole microbial genome sequencing projects, such as the genomes of Pseudomonas bathycetes, Bacillus thuringiensis, Thermoanaerobacter tengcongensis, Streptococcus suis, and quite a few virus genomes. In addition, our in-house Laboratory Information Management System (LIMS) as well as manual basecalling ensures the highest service quality.

CD Genomics has been offering professional DNA library construction services for over 5 years. Hundreds of various cDNA libraries (such as standard cDNA library, large insert cDNA library, normalized cDNA library and subtracted cDNA library) and genomic DNA libraries (including short-insert plasmid shotgun library, large-insert plasmid shotgun library, whole genome shotgun library, Fosmid library, Cosmid library, MiniBAC and BAC library) have been constructed in our lab

CD Genomics has been dedicated to provide a full range of services to develop high quality customized aptamers for research, diagnostic and therapeutic applications. Services offered by CD Genomics include aptamer synthesis, aptamer generation, cell aptamer selection, aptamer design and modification, negative selection and so on.

Years in service: 19

Other services offered by CD Genomics:

Service Description Price
Other Services We provide statistical and bioinformatic data analysis services that help explain the large amounts of data commonly generated by next generation sequencing and genotyping experiments. Our bioinformatic staff consists of all PhD-level scientists trained in bioinformatics, biology and statistics. The software infrastructure for analysis is a combination of custom-built and open-source software. O… Inquire
SNP / Indel Mapping CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost. Advantages of SNP Microarray Custom, flexible, and scalable; High call rates (> 99%) and high accuracy; Cost-… $80.00 USD (per sample)
Metagenomic Analysis Key Features and Advantages Longest average read lengths, with~50% of reads longer than 50kb, which exceeds the size of repetitive elements in the average bacterial genome. No DNA amplification. Highest consensus accuracy, low sequencing-context bias Novel bioinformatics analysis programs and pipelines Well-experienced personnel Sample Requirements: gDNA≥5 ug Sequencing Strategy: PacBio Platfo… 120.00

Bioinformatics Unit, Panacea Biosciences

NGS provider India

Other services offered by Bioinformatics Unit, Panacea Biosciences:

Service Description Price
Read Filtering and Cleaning $40.00 USD (per sample)
Exome Analysis End to End Exome-Seq Data Analysis $75.00 USD (per sample)
ChIP-Seq Analysis we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. $80.00 USD (per sample)
Genome Mapping Available only for Human, Mouse and available sequenced geneomes $75.00 USD (per sample)
SNP/SV/CNV Discovery End to End variant analysis $70.00 USD (per sample)
Small RNA Annotation Available only for Human, Mouse and available sequenced geneomes $60.00 USD (per sample)
Base Calling Base calling is the process of assigning bases (nucleobases) to chromatogram peaks. One computer program for accomplishing this job is Phred base-calling, which is a widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. $50.00 USD (per sample)

Dreamgenics

NGS provider Spain

Dreamgenics is a biotech company that offers bioinformatics analysis services for genomic, transcriptomic and metagenomic NGS data using our Genome One software. Genome One (CE-IVD certified) is an advanced tool that allows the integration of all the bioinformatics solutions required for the study, including read alignment, variant calling and annotation. Our analyses identify high-quality genomic variants through high sensitivity and specificity standards, extracting important biological information and reducing validation costs. The services that we offer are the following: WGS, WES, Gene panels, Transcriptomics (RNA-Seq) and Metagenomics. Additionally, we hand in the results using our web viewer Genome One Reports (https://www.dreamgenics.com/en/genome-one/).

The use of our bioinformatics tools allows us to offer you high-quality results in a fast and simple way. By using our analysis services, you considerably reduce costs and the investment in technological devices, informatics and qualified professionals.

Lastly, we are an ISO 9001:2015, UNE-EN ISO 13485:2018 and UNE-ISO/IEC 27001:2017 certified company which represents our commitment to provide our customers with products and services that meet the most demanding quality standards.

Years in service: 13

Other services offered by Dreamgenics:

Service Description Price
Single Cell RNA-Seq Analysis We offer Single cell RNA-Seq bioinformatic analysis from FASTQ files including: - Sequencing and mapping quality control. - Alignment of reads against reference genome. - Quantification of gene expression at the single cell level. - Reduction of data dimensionality. - Clustering or division of cells into different groups and subgroups. - Differential gene expression analysis. - Study of the evol… $200.00 USD (per sample)
Differential Gene Expression Analysis Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)
Exome Analysis Our bioinformatics analysis includes: Quality control, Alignment, Detection of high quality variants (SNVs, translocations and CNVs), Filtering of common variants, Annotation of variants obtained with multiple databases and prediction algorithms and Comparison between samples and extraction of recurrent variants. We will deliver the results to the Genohub data bucket as well as through our platf… $80.00 USD (per sample)
Transcriptome Annotation Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)

genexa Ltd

Switzerland

genexa is a genomic data analysis provider located in Switzerland. Our bioinformatics services are centered around de novo assembly of genomes and metagenomes. We focus on processing, analysis, and interpretation of your genomics data. For all our fields of expertise, we offer to perform the entire analysis workflow from raw data to documentation, but also consulting and troubleshooting if required. genexa also provides resources to run computationally demanding tasks for specific jobs if you have an existing analysis workflow, but lack the computational resources to run it on large amounts of data. For further information check: genexa.ch

Years in service: 10

Other services offered by genexa Ltd:

Service Description Price
Differential Gene Expression Analysis Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Other Services We offer bioinformatics services using long-read sequencing (PacBio & Oxford Nanopore Technologies). We have several years of experience using third-gen. technologies, mainly applying these technologies for de novo assembly of individual genomes and metagenomes. We also offer transcriptomic analyses using long-read technologies. If you want to start using PacBio or Oxford Nanopore Technologies,… Inquire
Read Filtering and Cleaning Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire
Base Calling Inquire
Microbiome Analysis Inquire